Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011650.1 Kokia drynarioides strain JFW-HI SEQ_126642, 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: 48224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 376 characters in sequence are not A, C, G, or T
Found at i:13284 original size:22 final size:21
Alignment explanation
Indices: 13253--13309 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
13243 GGTATTGAAA
13253 TTTAT-TTTAAATATATAATG
1 TTTATATTTAAATATATAATG
* * *
13273 TTATATATTTAAATTTTTATTG
1 TT-TATATTTAAATATATAATG
*
13295 TTTATATTTTAATAT
1 TTTATATTTAAATAT
13310 TTAAGATCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.07
21 14 0.47
22 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
TTTATATTTAAATATATAATG
Found at i:18063 original size:18 final size:18
Alignment explanation
Indices: 18040--18075 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18030 AGATGAAAAG
18040 TCACGTGGCTGACGTGGA
1 TCACGTGGCTGACGTGGA
18058 TCACGTGGCTGACGTGGA
1 TCACGTGGCTGACGTGGA
18076 GCTTGCTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.39, T:0.22
Consensus pattern (18 bp):
TCACGTGGCTGACGTGGA
Found at i:18085 original size:15 final size:16
Alignment explanation
Indices: 18065--18105 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
18055 GGATCACGTG
18065 GCTGACGTGGAGC-T-T
1 GCTGACGTGGA-CATAT
18080 GCTGACGTGGACATAT
1 GCTGACGTGGACATAT
18096 GCTGACGTGG
1 GCTGACGTGG
18106 TATGATGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.04
15 12 0.50
16 11 0.46
ACGTcount: A:0.17, C:0.20, G:0.39, T:0.24
Consensus pattern (16 bp):
GCTGACGTGGACATAT
Found at i:23001 original size:21 final size:21
Alignment explanation
Indices: 22914--22992 Score: 140
Period size: 21 Copynumber: 3.8 Consensus size: 21
22904 CACCAACTGA
*
22914 GACGTCGATGACTCACCTTGT
1 GACGGCGATGACTCACCTTGT
22935 GACGGCGATGACTCACCTTGT
1 GACGGCGATGACTCACCTTGT
22956 GACGGCGATGACTCACCTTGT
1 GACGGCGATGACTCACCTTGT
*
22977 GACGTCGATGACTCAC
1 GACGGCGATGACTCAC
22993 TTTCCGACGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (21 bp):
GACGGCGATGACTCACCTTGT
Found at i:23002 original size:42 final size:42
Alignment explanation
Indices: 22914--23004 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
22904 CACCAACTGA
* **
22914 GACGTCGATGACTCACCTTGTGACGGCGATGACTCACCTTGT
1 GACGGCGATGACTCACCTTGTGACGGCGATGACTCACCTTCC
* *
22956 GACGGCGATGACTCACCTTGTGACGTCGATGACTCACTTTCC
1 GACGGCGATGACTCACCTTGTGACGGCGATGACTCACCTTCC
22998 GACGGCG
1 GACGGCG
23005 GAGAATCCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (42 bp):
GACGGCGATGACTCACCTTGTGACGGCGATGACTCACCTTCC
Found at i:24682 original size:40 final size:40
Alignment explanation
Indices: 24627--24707 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
24617 TTGAAAATTG
24627 AAAATAATTACTAATAGTCCACAGTTATGTTTTATAACAC
1 AAAATAATTACTAATAGTCCACAGTTATGTTTTATAACAC
* *
24667 AAAATAATTACTAATAGTCCACTGTTATTTTTTATAACAC
1 AAAATAATTACTAATAGTCCACAGTTATGTTTTATAACAC
24707 A
1 A
24708 CTTAGATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (40 bp):
AAAATAATTACTAATAGTCCACAGTTATGTTTTATAACAC
Found at i:25056 original size:32 final size:33
Alignment explanation
Indices: 25013--25081 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
25003 CTAAAGACTA
* *
25013 AAAATTATAAAATAGT-TTTTAATATTAAAATT
1 AAAATTATAAAATAATATTTTAACATTAAAATT
* *
25045 AAAATTTTAAAATAATATTTTAACATTAAATTT
1 AAAATTATAAAATAATATTTTAACATTAAAATT
25078 AAAA
1 AAAA
25082 ATATTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAATTATAAAATAATATTTTAACATTAAAATT
Found at i:25066 original size:13 final size:14
Alignment explanation
Indices: 25037--25083 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
25027 GTTTTTAATA
25037 TTAAAATTAAAATT
1 TTAAAATTAAAATT
*
25051 TTAAAA-TAATATT
1 TTAAAATTAAAATT
*
25064 TTAACATT-AAATT
1 TTAAAATTAAAATT
*
25077 TAAAAAT
1 TTAAAAT
25084 ATTTTGATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAATTAAAATT
Found at i:25261 original size:47 final size:47
Alignment explanation
Indices: 25207--25304 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 47
25197 AGACATTTAT
*
25207 ATAAATTTTCAAGATAATATTATTTTTTACCTTTACTTAAATTCATA
1 ATAAATTTTCAAGATAAAATTATTTTTTACCTTTACTTAAATTCATA
25254 ATAAATTTTCAAGATAAAATTATTTTTTACCTTTACTTAAATTCATA
1 ATAAATTTTCAAGATAAAATTATTTTTTACCTTTACTTAAATTCATA
25301 ATAA
1 ATAA
25305 GTGTTGAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (47 bp):
ATAAATTTTCAAGATAAAATTATTTTTTACCTTTACTTAAATTCATA
Found at i:29057 original size:2 final size:2
Alignment explanation
Indices: 29050--29074 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29040 ACTTAATTGA
29050 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29075 AAGATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29517 original size:24 final size:24
Alignment explanation
Indices: 29481--29526 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
29471 CCTTCAAACT
* *
29481 TATTTAAACTATATTATTATTTGC
1 TATTTAAACTATAATATAATTTGC
**
29505 TATTTAAGGTATAATATAATTT
1 TATTTAAACTATAATATAATTT
29527 TTTTATTTGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (24 bp):
TATTTAAACTATAATATAATTTGC
Found at i:43881 original size:16 final size:17
Alignment explanation
Indices: 43848--43881 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43838 ATGTTTTTAT
43848 AATTAAATATTAATAAA
1 AATTAAATATTAATAAA
*
43865 AATTAATTATT-ATAAA
1 AATTAAATATTAATAAA
43881 A
1 A
43882 CAAGCTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATATTAATAAA
Found at i:45106 original size:29 final size:28
Alignment explanation
Indices: 45056--45114 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
45046 TACGTGATAG
* *
45056 ATAATTGTTGCTCTCTACATAATATAAAA
1 ATAATTATTGCTCTCTACATAAGA-AAAA
* **
45085 ATAATTATTGCTCTTTGTATAAGAAAAA
1 ATAATTATTGCTCTCTACATAAGAAAAA
45113 AT
1 AT
45115 GAAATAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (28 bp):
ATAATTATTGCTCTCTACATAAGAAAAA
Found at i:46091 original size:22 final size:20
Alignment explanation
Indices: 46061--46112 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
46051 TTTTAAGTTT
*
46061 ATAAGTATAAAAGCAATATGTC
1 ATAAATATAAAAGCAAT-TG-C
46083 ATAAATATAAAA-CAATTGC
1 ATAAATATAAAAGCAATTGC
46102 --AAATATAAAAG
1 ATAAATATAAAAG
46113 TACATTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 10 0.36
19 1 0.04
20 2 0.07
21 4 0.14
22 11 0.39
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.25
Consensus pattern (20 bp):
ATAAATATAAAAGCAATTGC
Found at i:47527 original size:2 final size:2
Alignment explanation
Indices: 47520--47549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47510 GTTATGAGTA
47520 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
47550 GTGAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.