Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005302.1 Kokia drynarioides strain JFW-HI SEQ_119231, 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: 68734
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:5370 original size:18 final size:20
Alignment explanation
Indices: 5337--5376 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5327 AATTTGTGTC
5337 ATATATTTGACATAATT-TT
1 ATATATTTGACATAATTCTT
*
5356 ATATTTTTG-CATAATTCTT
1 ATATATTTGACATAATTCTT
5375 AT
1 AT
5377 TGTGTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
ATATATTTGACATAATTCTT
Found at i:5377 original size:17 final size:19
Alignment explanation
Indices: 5337--5377 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
5327 AATTTGTGTC
* *
5337 ATATATTTGACATAATTTT
1 ATATTTTTGACATAATTCT
5356 ATATTTTTG-CATAATTCT
1 ATATTTTTGACATAATTCT
5374 -TATT
1 ATATT
5378 GTGTTTGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (19 bp):
ATATTTTTGACATAATTCT
Found at i:6220 original size:2 final size:2
Alignment explanation
Indices: 6213--6247 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6203 AAATATTTTA
6213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6248 GTAAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11335 original size:23 final size:21
Alignment explanation
Indices: 11309--11354 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11299 AATAACTTGA
11309 TTAACTCAAATAATTTGAACTAT
1 TTAACTC-AA-AATTTGAACTAT
* *
11332 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAATTTGAACTAT
11353 TT
1 TT
11355 TTCGACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAATTTGAACTAT
Found at i:13086 original size:17 final size:18
Alignment explanation
Indices: 13064--13102 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13054 ATATGTTCAT
*
13064 GAAAAAG-TAACTCTCAA
1 GAAAAAGTTAAATCTCAA
*
13081 GAAAAAGTTAAATTTCAA
1 GAAAAAGTTAAATCTCAA
13099 GAAA
1 GAAA
13103 TGTAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (18 bp):
GAAAAAGTTAAATCTCAA
Found at i:13098 original size:18 final size:17
Alignment explanation
Indices: 13059--13102 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
13049 CATTGATATG
* *
13059 TTCATGAAAAAGTAACT
1 TTCAAGAAAAAGTAAAT
*
13076 CTCAAGAAAAAGTTAAAT
1 TTCAAGAAAAAG-TAAAT
13094 TTCAAGAAA
1 TTCAAGAAA
13103 TGTAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (17 bp):
TTCAAGAAAAAGTAAAT
Found at i:22837 original size:257 final size:258
Alignment explanation
Indices: 22318--22837 Score: 819
Period size: 256 Copynumber: 2.0 Consensus size: 258
22308 ATATGCATAT
* *
22318 TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATTATTAACCAGACCGATCCAAAAT
1 TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATCATTAACCAGACCGATCCAAAAC
* *
22383 CACTTAAATTAAGAACAATAAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTT
66 CACTTAAACTAAG-A-AAGAAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTT
*
22448 TAAACAAACAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACTAAACAGA
129 TAAACAAAAAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACTAAACAGA
* * *
22513 GATCGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGACGCCACCGA
194 GATCGAGAAGAAGATCCAGCATCGTCTCGCAGTTTTTCCCTCGGTTTTTCCTTCGACGCCACCGA
* * * *
22578 TCCATATAGAATTCAAGATCATTGCAACTATTATGATTCTATCATTAACCAGACCGATTCAAAAC
1 TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATCATTAACCAGACCGATCCAAAAC
* * * *
22643 CACTTAAACTAAG-GAGGAAAATAAA-GAGTTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTA
66 CACTTAAACTAAGAAAGAAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTA
** *
22706 AACAAAAAATTGGAGTAATATTTAAACATGATAATTATGCAAGTAATTAGGGTACCTAAACAGAG
131 AACAAAAAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTA-CTAAACAGAG
*
22771 GTCGAGAAGAAGATCCAGCATCGTCTCGCAGTTTTTCCCTCGGTTTTTCCTTCGACGCCACCGA
195 ATCGAGAAGAAGATCCAGCATCGTCTCGCAGTTTTTCCCTCGGTTTTTCCTTCGACGCCACCGA
22835 TCC
1 TCC
22838 TCCCCTACCC
Statistics
Matches: 239, Mismatches: 20, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
256 87 0.36
257 81 0.34
260 71 0.30
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (258 bp):
TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATCATTAACCAGACCGATCCAAAAC
CACTTAAACTAAGAAAGAAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTA
AACAAAAAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACTAAACAGAGA
TCGAGAAGAAGATCCAGCATCGTCTCGCAGTTTTTCCCTCGGTTTTTCCTTCGACGCCACCGA
Found at i:28940 original size:1 final size:1
Alignment explanation
Indices: 28934--28963 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
28924 TAACAACAGG
28934 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28964 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33841 original size:33 final size:33
Alignment explanation
Indices: 33799--33868 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
33789 CCTGGAAATC
*
33799 ATGGGGATGTTAAAGGATTTAAAATGCATGGAA
1 ATGGGGATGTTAAAGGATTTAAAATCCATGGAA
* *
33832 ATGGGGATGTTAGAGGATTTAGAATCCATGGAA
1 ATGGGGATGTTAAAGGATTTAAAATCCATGGAA
33865 ATGG
1 ATGG
33869 AAACATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.04, G:0.33, T:0.27
Consensus pattern (33 bp):
ATGGGGATGTTAAAGGATTTAAAATCCATGGAA
Found at i:36794 original size:46 final size:46
Alignment explanation
Indices: 36741--36837 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
36731 TTAAAAAAAA
36741 TTAAAAACTATGATCTTATCTACACGTAAATTAAAATTTTCGATAG
1 TTAAAAACTATGATCTTATCTACACGTAAATTAAAATTTTCGATAG
*
36787 TTAAAAACTATGATCTTATCTACACTTAAATTAAAATTTTCGATAG
1 TTAAAAACTATGATCTTATCTACACGTAAATTAAAATTTTCGATAG
36833 TTAAA
1 TTAAA
36838 GTACAAGTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (46 bp):
TTAAAAACTATGATCTTATCTACACGTAAATTAAAATTTTCGATAG
Found at i:42985 original size:33 final size:34
Alignment explanation
Indices: 42907--42988 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 34
42897 GCTATCTGAA
42907 GGTGGTGATGATTGTTGCTTAGAAGGAGGAGGTGGT
1 GGTGGTGATGATTGTTGCTT--AAGGAGGAGGTGGT
* *
42943 GAATTTGGTGATGATTGTTGCTT-AGGAGGTGGTGGT
1 G---GTGGTGATGATTGTTGCTTAAGGAGGAGGTGGT
42979 GGTGGTGATG
1 GGTGGTGATG
42989 GTGACGGTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
33 8 0.20
36 14 0.35
39 18 0.45
ACGTcount: A:0.17, C:0.02, G:0.46, T:0.34
Consensus pattern (34 bp):
GGTGGTGATGATTGTTGCTTAAGGAGGAGGTGGT
Found at i:43074 original size:15 final size:15
Alignment explanation
Indices: 43056--43088 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43046 ATTGTTCCCG
43056 AGGAGGAGGAGGAGA
1 AGGAGGAGGAGGAGA
*
43071 AGGAGGAGGAGGTGA
1 AGGAGGAGGAGGAGA
43086 AGG
1 AGG
43089 TGGTGGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (15 bp):
AGGAGGAGGAGGAGA
Found at i:44401 original size:22 final size:22
Alignment explanation
Indices: 44352--44401 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
44342 TGAAATAGTG
* * *
44352 AGAAAATAATTAGAAAATAGCA
1 AGAAAATAATAAGAAAAAAACA
* *
44374 ACAAAATAATAATAAAAAAACA
1 AGAAAATAATAAGAAAAAAACA
44396 AGAAAA
1 AGAAAA
44402 CATCAATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (22 bp):
AGAAAATAATAAGAAAAAAACA
Found at i:51359 original size:13 final size:14
Alignment explanation
Indices: 51341--51373 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
51331 TAAAATAAGG
51341 ATAAAATA-AAAGA
1 ATAAAATATAAAGA
51354 ATAAAATATAAAGA
1 ATAAAATATAAAGA
51368 A-AAAAT
1 ATAAAAT
51374 GATTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (14 bp):
ATAAAATATAAAGA
Found at i:52176 original size:30 final size:29
Alignment explanation
Indices: 52113--52177 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
52103 TACAAATTTG
* *
52113 AAATTTAGTCTTTGTACTTTTATTTTCGG
1 AAATTTAGTCTTTGTACTTTTAATTTCGA
52142 AAATTTAGTCTCTT-TACTTTTTAGATTTC-A
1 AAATTTAGTCT-TTGTAC-TTTTA-ATTTCGA
52172 AAATTT
1 AAATTT
52178 CAGGTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 14 0.45
30 13 0.42
31 4 0.13
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (29 bp):
AAATTTAGTCTTTGTACTTTTAATTTCGA
Found at i:53290 original size:20 final size:21
Alignment explanation
Indices: 53251--53291 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53241 ACAACAAAAT
53251 TAAATTAATTCTAAATTAACAC
1 TAAATTAATTCT-AATTAACAC
*
53273 TAAATTTATTCT-ATTAACA
1 TAAATTAATTCTAATTAACA
53292 AAATCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTAATTCTAATTAACAC
Found at i:56004 original size:17 final size:17
Alignment explanation
Indices: 55978--56013 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55968 CCCAAATTAT
*
55978 ATATAAAATTTGATTCA
1 ATATAAAATTTAATTCA
*
55995 ATATACAATTTAATTCA
1 ATATAAAATTTAATTCA
56012 AT
1 AT
56014 GTAATTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATAAAATTTAATTCA
Found at i:56393 original size:31 final size:31
Alignment explanation
Indices: 56285--56394 Score: 80
Period size: 31 Copynumber: 3.5 Consensus size: 31
56275 TAATATACTA
*
56285 TTTGGTACTTGAGTTTAGCTTCAATATTCAAT
1 TTTGGTACTTGAGTTTAGCTTCAATGTTC-AT
* *** ** *
56317 TTT-GTA-TCTGTGTTTTTTTTTTATGTTTCAA
1 TTTGGTACT-TGAGTTTAGCTTCAATG-TTCAT
** *
56348 TTTGGTACCCGAGTTTGGCTTCAATGTTCAT
1 TTTGGTACTTGAGTTTAGCTTCAATGTTCAT
56379 TTTGGTACTTGAGTTT
1 TTTGGTACTTGAGTTT
56395 TCAATTGTCA
Statistics
Matches: 55, Mismatches: 19, Indels: 9
0.66 0.23 0.11
Matches are distributed among these distances:
30 1 0.02
31 35 0.64
32 19 0.35
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (31 bp):
TTTGGTACTTGAGTTTAGCTTCAATGTTCAT
Found at i:64731 original size:14 final size:14
Alignment explanation
Indices: 64712--64739 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64702 GACACACATG
64712 CATACATACATATA
1 CATACATACATATA
64726 CATACATACATATA
1 CATACATACATATA
64740 TATATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
CATACATACATATA
Found at i:64733 original size:18 final size:18
Alignment explanation
Indices: 64707--64743 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
64697 TGCTTGACAC
*
64707 ACATGCATACATACATAT
1 ACATACATACATACATAT
*
64725 ACATACATACATATATAT
1 ACATACATACATACATAT
64743 A
1 A
64744 TTAGATTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.30
Consensus pattern (18 bp):
ACATACATACATACATAT
Found at i:68264 original size:65 final size:65
Alignment explanation
Indices: 68158--68359 Score: 386
Period size: 65 Copynumber: 3.1 Consensus size: 65
68148 CCCCTACATT
68158 ATGGTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
1 ATGGTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
*
68223 ATGTTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
1 ATGGTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
68288 ATGGTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
1 ATGGTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
*
68353 AAGGTTT
1 ATGGTTT
68360 CAAGAATGGA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 134 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (65 bp):
ATGGTTTTCATAAATTTTCATAATTTTTTCTTGGTTAACCATATAAACACACACAACACAAACTC
Done.