Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008663.1 Kokia drynarioides strain JFW-HI SEQ_123345, 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: 33023
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:3602 original size:19 final size:19
Alignment explanation
Indices: 3578--3616 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3568 AAACAAACAC
3578 TTGGTTTTTTATGCTAGAA
1 TTGGTTTTTTATGCTAGAA
3597 TTGGTTTTTTATGCTAGAA
1 TTGGTTTTTTATGCTAGAA
3616 T
1 T
3617 GAAGATTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (19 bp):
TTGGTTTTTTATGCTAGAA
Found at i:7490 original size:13 final size:12
Alignment explanation
Indices: 7469--7505 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
7459 AATTTTGCTA
7469 TATGTAATTAAT
1 TATGTAATTAAT
*
7481 TATTTAAATTAAT
1 TATGT-AATTAAT
7494 TATGTAATTAAT
1 TATGTAATTAAT
7506 ATTATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATGTAATTAAT
Found at i:10272 original size:9 final size:9
Alignment explanation
Indices: 10260--10338 Score: 63
Period size: 9 Copynumber: 8.3 Consensus size: 9
10250 TTTTTTAAAT
10260 TTTAAAAAA
1 TTTAAAAAA
10269 TTTAAAAAA
1 TTTAAAAAA
* *
10278 -ATAAAAAC
1 TTTAAAAAA
10286 TATTAAAAAA
1 T-TTAAAAAA
10296 TTTAAAAACA
1 TTTAAAAA-A
*
10306 TATTAAAATTA
1 T-TTAAAA-AA
10317 TTT-AAAAA
1 TTTAAAAAA
10325 TTATAAAAATA
1 TT-TAAAAA-A
10336 TTT
1 TTT
10339 TTAAGAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 9 0.16
9 20 0.36
10 16 0.29
11 11 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:10323 original size:20 final size:19
Alignment explanation
Indices: 10260--10338 Score: 74
Period size: 19 Copynumber: 4.2 Consensus size: 19
10250 TTTTTTAAAT
*
10260 TTTAAAAAAT-TTAAAAAA
1 TTTAAAAACTATTAAAAAA
*
10278 -ATAAAAACTATTAAAAAA
1 TTTAAAAACTATTAAAAAA
*
10296 TTTAAAAACATATTAAAATTA
1 TTTAAAAAC-TATTAAAA-AA
*
10317 TTTAAAAATTA-TAAAAATA
1 TTTAAAAACTATTAAAAA-A
10336 TTT
1 TTT
10339 TTAAGAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
17 7 0.14
18 8 0.16
19 16 0.32
20 10 0.20
21 9 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAAAACTATTAAAAAA
Found at i:11957 original size:19 final size:20
Alignment explanation
Indices: 11933--11972 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11923 ATTTTAATAG
11933 ATTTTAAACATGT-ATTTGC
1 ATTTTAAACATGTGATTTGC
* *
11952 ATTTTAGATATGTGATTTGC
1 ATTTTAAACATGTGATTTGC
11972 A
1 A
11973 AGTGTGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (20 bp):
ATTTTAAACATGTGATTTGC
Found at i:14213 original size:14 final size:14
Alignment explanation
Indices: 14194--14223 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14184 CCAAACCGAA
14194 CTTTTGACCCAAAC
1 CTTTTGACCCAAAC
*
14208 CTTTTGACCTAAAC
1 CTTTTGACCCAAAC
14222 CT
1 CT
14224 AACCCGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (14 bp):
CTTTTGACCCAAAC
Found at i:24043 original size:15 final size:15
Alignment explanation
Indices: 24023--24055 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
24013 CTGACTTAAT
24023 AGTATTTGCACCTTA
1 AGTATTTGCACCTTA
24038 AGTATTTGCACCTTA
1 AGTATTTGCACCTTA
24053 AGT
1 AGT
24056 TTCATAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (15 bp):
AGTATTTGCACCTTA
Found at i:27111 original size:25 final size:23
Alignment explanation
Indices: 27083--27137 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
27073 TAATAATAGT
27083 TATATATATATATCAATACTTATAA
1 TATATATATATATCAATA--TATAA
* *
27108 TATATAT-TATTTCATTATATAA
1 TATATATATATATCAATATATAA
27130 TAT-TATAT
1 TATATATAT
27138 CACACACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.11
22 9 0.33
24 8 0.30
25 7 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATATATATATCAATATATAA
Found at i:27428 original size:16 final size:16
Alignment explanation
Indices: 27392--27430 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
27382 ATAATCTATG
*
27392 ATATAATAGTAGTTAT
1 ATATAATAGTAGTCAT
27408 ATATAATAGTAGTACATT
1 ATATAATAGTAGT-CA-T
27426 ATATA
1 ATATA
27431 TTATTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 1 0.05
18 6 0.30
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (16 bp):
ATATAATAGTAGTCAT
Done.