Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014943.1 Kokia drynarioides strain JFW-HI SEQ_129986, 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: 61048
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:4291 original size:16 final size:16
Alignment explanation
Indices: 4259--4288 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4249 AAAATTTTTG
4259 AGAAATAACCAAAAAT
1 AGAAATAACCAAAAAT
4275 AGAAAT-ACCAAAAA
1 AGAAATAACCAAAAA
4289 ATATAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (16 bp):
AGAAATAACCAAAAAT
Found at i:5269 original size:31 final size:30
Alignment explanation
Indices: 5230--5319 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
5220 GTAATTTAAG
*
5230 ATAT-AAATTTTGATTTTGATATAATTATAT
1 ATATGAAATTTTAATTTTGAT-TAATTATAT
* * *
5260 ATATGAAATTTTAATTGTGTTTTAAATATAT
1 ATATGAAATTTTAATTTTG-ATTAATTATAT
* *
5291 ATTTGAATTTTTAA-TTTGATTAAATTATA
1 ATATGAAATTTTAATTTTGATT-AATTATA
5320 AATTTTTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 2 0.04
30 13 0.27
31 32 0.67
32 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (30 bp):
ATATGAAATTTTAATTTTGATTAATTATAT
Found at i:5394 original size:23 final size:25
Alignment explanation
Indices: 5346--5394 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5336 AATACATCAT
* *
5346 ATTATTTTTATATTAGATAAATATA
1 ATTATTTGTATATTAGAAAAATATA
5371 ATTATTTGTATA-T-GAAAAATATA
1 ATTATTTGTATATTAGAAAAATATA
5394 A
1 A
5395 ACATAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 1 0.05
25 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
ATTATTTGTATATTAGAAAAATATA
Found at i:10259 original size:20 final size:20
Alignment explanation
Indices: 10231--10269 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10221 TCTGGAGACG
10231 AAAAATTTAAAAATAAAAAT
1 AAAAATTTAAAAATAAAAAT
* **
10251 AAAATTTTATCAATAAAAA
1 AAAAATTTAAAAATAAAAA
10270 GGAGAGCGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTTAAAAATAAAAAT
Found at i:17984 original size:2 final size:2
Alignment explanation
Indices: 17977--18014 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17967 CATTCAATCA
17977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18015 CAAGAAGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18765 original size:24 final size:24
Alignment explanation
Indices: 18720--18765 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18710 TTATGTATAG
*
18720 AGATTAATTTTTAACAGTAAAAAT
1 AGATTAATTTTTAACAGAAAAAAT
*
18744 AGATGTAATTTTT-ATAGAAAAA
1 AGAT-TAATTTTTAACAGAAAAA
18766 TCTGTTTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (24 bp):
AGATTAATTTTTAACAGAAAAAAT
Found at i:26790 original size:1 final size:1
Alignment explanation
Indices: 26784--26808 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
26774 NNNNNNNNNN
26784 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
26809 GTATTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37204 original size:6 final size:6
Alignment explanation
Indices: 37193--37219 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
37183 ATTAATCAAA
37193 ACTCTC ACTCTC ACTCTC ACTCTC ACT
1 ACTCTC ACTCTC ACTCTC ACTCTC ACT
37220 AATGCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
ACTCTC
Found at i:39938 original size:15 final size:16
Alignment explanation
Indices: 39903--39941 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
39893 ATAGTGAAAA
39903 TATAATTTATAATTTT
1 TATAATTTATAATTTT
*
39919 AATAATTTAT-ATTTT
1 TATAATTTATAATTTT
39934 TATAATTT
1 TATAATTT
39942 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATAATTTT
Found at i:48262 original size:18 final size:17
Alignment explanation
Indices: 48239--48273 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
48229 ATTTTCTTTT
48239 AAAAATGAGTAAATTTAC
1 AAAAAT-AGTAAATTTAC
*
48257 AAAAATCGTAAATTTAC
1 AAAAATAGTAAATTTAC
48274 CTTTTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAAATAGTAAATTTAC
Found at i:50445 original size:17 final size:16
Alignment explanation
Indices: 50423--50501 Score: 79
Period size: 16 Copynumber: 4.6 Consensus size: 16
50413 GTCAACTAAT
50423 AATTTAAAAATGATAAA
1 AATTTAAAAAT-ATAAA
50440 AATTTAAAAACT-TAAA
1 AATTTAAAAA-TATAAA
* *
50456 AAATTAAAAATTAAAAA
1 AATTTAAAAA-TATAAA
50473 TAATTTTAAAAAATATAAA
1 -AA-TTT-AAAAATATAAA
50492 AATTTAAAAA
1 AATTTAAAAA
50502 ATTAATAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
16 19 0.37
17 16 0.31
18 5 0.10
19 7 0.13
20 5 0.10
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (16 bp):
AATTTAAAAATATAAA
Found at i:50447 original size:8 final size:8
Alignment explanation
Indices: 50423--50506 Score: 69
Period size: 8 Copynumber: 9.9 Consensus size: 8
50413 GTCAACTAAT
50423 AATTTAAA
1 AATTTAAA
*
50431 AATGATAAA
1 AAT-TTAAA
50440 AATTTAAA
1 AATTTAAA
*
50448 AACTTAAA
1 AATTTAAA
*
50456 AAATTAAA
1 AATTTAAA
*
50464 AATTAAAAA
1 AATT-TAAA
50473 TAATTTTAAAA
1 -AA-TTT-AAA
*
50484 AATATAAA
1 AATTTAAA
50492 AATTTAAA
1 AATTTAAA
*
50500 AAATTAA
1 AATTTAA
50507 TAACATAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
8 40 0.66
9 12 0.20
10 4 0.07
11 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (8 bp):
AATTTAAA
Found at i:50471 original size:6 final size:7
Alignment explanation
Indices: 50426--50473 Score: 51
Period size: 7 Copynumber: 6.1 Consensus size: 7
50416 AACTAATAAT
50426 TTAAAAA
1 TTAAAAA
50433 TGATAAAAA
1 T--TAAAAA
50442 TTTAAAAA
1 -TTAAAAA
50450 CTTAAAAAA
1 -TT-AAAAA
50459 TTAAAAA
1 TTAAAAA
50466 TTAAAAA
1 TTAAAAA
50473 T
1 T
50474 AATTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 14 0.39
8 10 0.28
9 11 0.31
10 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:50502 original size:17 final size:17
Alignment explanation
Indices: 50423--50503 Score: 85
Period size: 17 Copynumber: 4.7 Consensus size: 17
50413 GTCAACTAAT
50423 AATTT-AAAAATGATAAA
1 AATTTAAAAAAT-ATAAA
*
50440 AATTTAAAAACT-TAAA
1 AATTTAAAAAATATAAA
* * *
50456 AAATTAAAAATTAAAAA
1 AATTTAAAAAATATAAA
50473 TAATTTTAAAAAATATAAA
1 -AA-TTTAAAAAATATAAA
50492 AATTTAAAAAAT
1 AATTTAAAAAAT
50504 TAATAACATA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
16 14 0.26
17 18 0.34
18 9 0.17
19 12 0.23
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (17 bp):
AATTTAAAAAATATAAA
Found at i:50858 original size:13 final size:11
Alignment explanation
Indices: 50840--50878 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
50830 TTTTAGAGAA
50840 AAAAGAAAAAGGG
1 AAAAGAAAAA--G
50853 AAAAGAAAAAG
1 AAAAGAAAAAG
50864 AAAAG-AAAAG
1 AAAAGAAAAAG
50874 AAAAG
1 AAAAG
50879 GGAAGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.38
11 6 0.23
13 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:58058 original size:29 final size:33
Alignment explanation
Indices: 58002--58075 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 33
57992 TTCAATATAC
*
58002 AAATTTTAACAATATTAATAATTGAATTTGAA-TT
1 AAATTTTAACAATATT-ATAATTGAA-TTCAACTT
58036 AAATTTTAACAATA-T-TAA-T-AATTCAACTT
1 AAATTTTAACAATATTATAATTGAATTCAACTT
58065 AAATTTTAACA
1 AAATTTTAACA
58076 TCTCAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 4 0.11
29 15 0.39
30 1 0.03
31 3 0.08
33 1 0.03
34 14 0.37
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (33 bp):
AAATTTTAACAATATTATAATTGAATTCAACTT
Found at i:58448 original size:18 final size:18
Alignment explanation
Indices: 58425--58460 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58415 GATATTTTAA
*
58425 ATTTTTTAAAAATTAAAT
1 ATTTTTTAAAAATAAAAT
*
58443 ATTTTTTTAAAATAAAAT
1 ATTTTTTAAAAATAAAAT
58461 GGGTCAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTTAAAAATAAAAT
Done.