Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007481.1 Kokia drynarioides strain JFW-HI SEQ_122104, 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: 22671
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2250 original size:41 final size:41
Alignment explanation
Indices: 2150--2323 Score: 222
Period size: 41 Copynumber: 4.2 Consensus size: 41
2140 TTGTATAAAT
* *
2150 GGAAAACTCATGTCTCGAAATGAGAATGAGATTTTGATTTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGA-TTAA
* * * * *
2192 AGAAGACTCATGTCTCGAGATGAGAATAAGATTATGAATGA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* *
2233 GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTCATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* * *
2274 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATT-AA
2316 GGAAGACT
1 GGAAGACT
2324 ACTGACTCAA
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 70 0.62
42 42 0.38
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
Found at i:2253 original size:83 final size:82
Alignment explanation
Indices: 2150--2309 Score: 266
Period size: 82 Copynumber: 1.9 Consensus size: 82
2140 TTGTATAAAT
*
2150 GGAAAACTCATGTCTCGAAATGAGAATGAGATTTTGATTTAAAGAAGACTCATGTCTCGAGATGA
1 GGAAAACTCATGTCTCGAAATGAGAATGAGATTTTCA-TTAAAGAAGACTCATGTCTCGAGATGA
*
2215 GAATAAGATTATGAATGA
65 GAATAAGAATATGAATGA
* *
2233 GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTCATTAAGGAAGACTCATGTCTCGAGATGAG
1 GGAAAACTCATGTCTCGAAATGAGAATGAGATTTTCATTAAAGAAGACTCATGTCTCGAGATGAG
*
2298 AATGAGAATATG
66 AATAAGAATATG
2310 GTTAAAGGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
82 37 0.51
83 35 0.49
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (82 bp):
GGAAAACTCATGTCTCGAAATGAGAATGAGATTTTCATTAAAGAAGACTCATGTCTCGAGATGAG
AATAAGAATATGAATGA
Found at i:2319 original size:83 final size:84
Alignment explanation
Indices: 2104--2323 Score: 284
Period size: 83 Copynumber: 2.6 Consensus size: 84
2094 GGTGTATAAA
* * * * *
2104 AAGGAAGACTCATGTCTCGGGTTTGAGCATGAGAA-ATTGTATAAATGGAAAACTCATGTCTCGA
1 AAGGAAGACTCATGTCTCGAG-ATGAGAATGAGAATATGGT-TAAA-GGAAGACTCATGTCTCGA
*
2168 AATGAGAATGAGATTTTGATTT
63 AATGAGAATGAGATTTTCATTT
* * * ** *
2190 AAAGAAGACTCATGTCTCGAGATGAGAATAAGATTATGAAT-GAGGAAGACTCATGTCTCGAAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAAGGAAGACTCATGTCTCGAAAT
2254 GAGAATGAGATTTTCA-TT
66 GAGAATGAGATTTTCATTT
2272 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAAGGAAGACT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAAGGAAGACT
2324 ACTGACTCAA
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
82 38 0.33
83 44 0.39
84 1 0.01
85 10 0.09
86 21 0.18
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (84 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAAGGAAGACTCATGTCTCGAAAT
GAGAATGAGATTTTCATTT
Found at i:8200 original size:30 final size:30
Alignment explanation
Indices: 8166--8326 Score: 163
Period size: 30 Copynumber: 5.5 Consensus size: 30
8156 TCCTCAAACT
*
8166 TTTTGACCCCCAAAATTTTCCAAAATTACA
1 TTTTGAACCCCAAAATTTTCCAAAATTACA
* * *
8196 TTTTGATCCTCAAACTTTTCCAAAATTACA
1 TTTTGAACCCCAAAATTTTCCAAAATTACA
* *
8226 TTTT-AACCCTAAAATTTTCCTAAAATTAAA
1 TTTTGAACCCCAAAATTTTCC-AAAATTACA
*
8256 TTTTG-ACCCCTAAA-TTTCCTAAAATTACA
1 TTTTGAACCCCAAAATTTTCC-AAAATTACA
** * *
8285 -TTT-AACCCTTAAACTTCCCAAAATTACA
1 TTTTGAACCCCAAAATTTTCCAAAATTACA
8313 TTTTG-ACCCCAAAA
1 TTTTGAACCCCAAAA
8327 ACACATTTTG
Statistics
Matches: 110, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
28 20 0.18
29 40 0.36
30 50 0.45
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTTGAACCCCAAAATTTTCCAAAATTACA
Found at i:8280 original size:59 final size:58
Alignment explanation
Indices: 8177--8322 Score: 190
Period size: 58 Copynumber: 2.5 Consensus size: 58
8167 TTTGACCCCC
*
8177 AAAATTTTCCAAAATTACATTTTGA-TCCTCAAACTTTTCCAAAATTACATTTTAACCCT
1 AAAATTTTCCAAAATTACATTTTGACCCCTCAAAC-TTTCCAAAATTACA-TTTAACCCT
*
8236 AAAATTTTCCTAAAATTAAATTTTGACCCCT-AAA-TTTCCTAAAATTACATTTAACCCT
1 AAAATTTTCC-AAAATTACATTTTGACCCCTCAAACTTTCC-AAAATTACATTTAACCCT
* * *
8294 TAAACTTCCCAAAATTACATTTTGACCCC
1 AAAATTTTCCAAAATTACATTTTGACCCC
8323 AAAAACACAT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
57 18 0.23
58 21 0.27
59 19 0.24
60 17 0.22
61 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (58 bp):
AAAATTTTCCAAAATTACATTTTGACCCCTCAAACTTTCCAAAATTACATTTAACCCT
Found at i:8383 original size:76 final size:76
Alignment explanation
Indices: 8255--8398 Score: 229
Period size: 76 Copynumber: 1.9 Consensus size: 76
8245 CTAAAATTAA
*
8255 ATTTTGACCCCTAAATTTCCTAAAATTACATTTAACCCTTAAACTTCCCAAAATTACATTTTGAC
1 ATTTTGACCCCTAAATTTCCTAAAATTACATTTAACCCTTAAACTTCCCAAAATTACATTTTCAC
8320 CCCAAAAACAC
66 CCCAAAAACAC
**
8331 ATTTTGACCCC-AAACTTTCCTAAAATTACATTCTAACCC-TAAACTTTTCAAAATTACATTTTC
1 ATTTTGACCCCTAAA-TTTCCTAAAATTACATT-TAACCCTTAAACTTCCCAAAATTACATTTTC
8394 ACCCC
64 ACCCC
8399 GAATTCTTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
75 3 0.05
76 54 0.86
77 6 0.10
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (76 bp):
ATTTTGACCCCTAAATTTCCTAAAATTACATTTAACCCTTAAACTTCCCAAAATTACATTTTCAC
CCCAAAAACAC
Found at i:8397 original size:28 final size:29
Alignment explanation
Indices: 8329--8398 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
8319 CCCCAAAAAC
*
8329 ACATTTTGACCCCAAACTTTCCTAAAATT
1 ACATTTTAACCCCAAACTTTCCTAAAATT
* * *
8358 ACATTCTAACCCTAAACTTTTC-AAAATT
1 ACATTTTAACCCCAAACTTTCCTAAAATT
*
8386 ACATTTTCACCCC
1 ACATTTTAACCCC
8399 GAATTCTTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 16 0.47
29 18 0.53
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.34
Consensus pattern (29 bp):
ACATTTTAACCCCAAACTTTCCTAAAATT
Found at i:9634 original size:22 final size:23
Alignment explanation
Indices: 9608--9650 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
9598 AATTGGAAAT
* *
9608 AAAATTATTTTATTA-TTTTAAA
1 AAAATAATTTTAATAGTTTTAAA
9630 AAAATAATTTTAATAGTTTTA
1 AAAATAATTTTAATAGTTTTA
9651 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AAAATAATTTTAATAGTTTTAAA
Found at i:13377 original size:12 final size:11
Alignment explanation
Indices: 13345--13373 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
13335 AAATATTAAA
13345 TTAAAAATAAT
1 TTAAAAATAAT
13356 TTAAAAATAAT
1 TTAAAAATAAT
13367 TTAAAAA
1 TTAAAAA
13374 ATAAAAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAATAAT
Found at i:13643 original size:16 final size:16
Alignment explanation
Indices: 13622--13656 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13612 CAAACTGTTC
*
13622 ACAACTAACCTTCTTG
1 ACAACTAACCTTCATG
13638 ACAACTAACCTTCATG
1 ACAACTAACCTTCATG
13654 ACA
1 ACA
13657 CACGTCTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.31, G:0.06, T:0.26
Consensus pattern (16 bp):
ACAACTAACCTTCATG
Found at i:19360 original size:36 final size:37
Alignment explanation
Indices: 19307--19384 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 37
19297 TAAAAATGGA
* *
19307 TATAA-AAATTTTCAAAATCAATGAAAGAACTCAAAT
1 TATAATAAATTTTCAAAATAAATGAAAGAACTAAAAT
* * *
19343 TATAATAAATTTT-AAAATAAATTAAAGTATTAAAAT
1 TATAATAAATTTTCAAAATAAATGAAAGAACTAAAAT
19379 TATAAT
1 TATAAT
19385 CACGATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 29 0.81
37 7 0.19
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (37 bp):
TATAATAAATTTTCAAAATAAATGAAAGAACTAAAAT
Found at i:19635 original size:49 final size:51
Alignment explanation
Indices: 19540--19641 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 51
19530 TAATTTAAGT
*
19540 ATAATTTTTTAAATATTTCAATAATTTAAATAGAAACTATTGAATAATTTA
1 ATAATTTTTTAAATATTTCAATAATTAAAATAGAAACTATTGAATAATTTA
* *
19591 ATAATTTTTTAAA-A-TT-AATTAATTAAAATATAAATTTATT-AATAATTTA
1 ATAATTTTTTAAATATTTCAA-TAATTAAAATAGAAA-CTATTGAATAATTTA
19640 AT
1 AT
19642 GGTTTTAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
48 2 0.04
49 26 0.57
50 5 0.11
51 13 0.28
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (51 bp):
ATAATTTTTTAAATATTTCAATAATTAAAATAGAAACTATTGAATAATTTA
Found at i:20156 original size:28 final size:30
Alignment explanation
Indices: 20123--20192 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 30
20113 TTTGATTTTT
*
20123 TTTTTTTTAAGATTAATAATTATATTCGAC
1 TTTTTTTAAAGATTAATAATTATATTCGAC
* *
20153 TTTTTTTCAAAGATTAATAATTATATTTGAT
1 TTTTTTT-AAAGATTAATAATTATATTCGAC
20184 TTTTTTTAA
1 TTTTTTTAA
20193 TATTGAGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 9 0.25
31 27 0.75
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (30 bp):
TTTTTTTAAAGATTAATAATTATATTCGAC
Found at i:22284 original size:47 final size:48
Alignment explanation
Indices: 22190--22284 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
22180 TTAAAATTTT
* *
22190 CTCTTCACATCTCTGCAACCCCTGCTGCTATTATTTTTTTCCGGCAAC
1 CTCTTCACATCTCTGCAACCCCTGCTACTATTATTTTTTTCCAGCAAC
*
22238 CTCTTCACGTC-CTGCAACCCCCTGCTACTATTATTTTTTT-CAGCAAC
1 CTCTTCACATCTCTGCAA-CCCCTGCTACTATTATTTTTTTCCAGCAAC
22285 AACTTTGCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 12 0.28
48 31 0.72
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.37
Consensus pattern (48 bp):
CTCTTCACATCTCTGCAACCCCTGCTACTATTATTTTTTTCCAGCAAC
Done.