Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004456.1 Kokia drynarioides strain JFW-HI SEQ_117864, 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: 35481
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:4383 original size:33 final size:33
Alignment explanation
Indices: 4344--4410 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
4334 TGCATATATA
* *
4344 ATGTGGTCTACTGTAAAACCTTACATATATGCC
1 ATGTGGTCTACTATAAAACCTTACATACATGCC
* * *
4377 ATGTGGTGTATTATAAATCCTTACATACATGCC
1 ATGTGGTCTACTATAAAACCTTACATACATGCC
4410 A
1 A
4411 ATGACCATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (33 bp):
ATGTGGTCTACTATAAAACCTTACATACATGCC
Found at i:4580 original size:13 final size:13
Alignment explanation
Indices: 4562--4587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4552 ATAACTCATT
4562 TACACCAACCCAA
1 TACACCAACCCAA
4575 TACACCAACCCAA
1 TACACCAACCCAA
4588 GTTCCCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (13 bp):
TACACCAACCCAA
Found at i:8891 original size:322 final size:320
Alignment explanation
Indices: 8254--8878 Score: 796
Period size: 322 Copynumber: 1.9 Consensus size: 320
8244 TATTAAAATT
* * * * *
8254 TTGAAATCTCGAGTGAAGTTTAAAATACGATCCTTTGCACGTAACTTATTTCGCTTGATTTTAAA
1 TTGAAATCTCGAATGAAGTTTAAAATACGATCCTTCGCACATAACTTATTTCACGTGATTTTAAA
8319 AAACATCAAATTTGAGAAAAAACACCCGTGTGTTTCGAATTTCTTGGAAAATTGAAGTCATGTCC
66 AAACATCAAATTTGAGAAAAAACACCCGTGTGTTTCGAATTTCTTGGAAAATTGAAGTCATGTCC
* * * * * *
8384 AACACGTTAGGACACGATGTTCTCGGAATTTCGAAATTGAAGGATATTTTGAAAATTTTTAAAGA
131 AACACATTAGGACACGATGTTCTCGGAATTTCAAAATTGAAGGACACTTTGAAAAGTTTTAAAAA
* * *
8449 GGATATTCGATCGCACGAATTATACGAAAAATCATACCCAGCACGTTAGGTCATAATTTTTAGAA
196 GGATATTCGATCGCACGAATTATACGAAAAATCACACCCAACACGTTAGGGCATAATTTTTAGAA
8514 ACTTTCACACGAAAGGATATTACCTCGTTTTAGTTTAAAATTATTTGAATATTTTTTGAGGAC
261 ACTTTCACACGAAAGGATATTACCTCGTTTTAG--T-AAATTATTTGAATATTTTTTGAGGAC
*
8577 TTGAAATTTCGAATGAAGTTTAAAATACGATCC-TCGAACACATAACTTATTTCACGTGATTTT-
1 TTGAAATCTCGAATGAAGTTTAAAATACGATCCTTCG--CACATAACTTATTTCACGTGATTTTA
* * * ** * * *
8640 CAAAA-ATTAGATTTGA-AGAAAAATGCTCGTGTGTTTCGAATTT-TTCGGAGAATTGAAGTCGT
64 AAAAACATCAAATTTGAGA-AAAAACACCCGTGTGTTTCGAATTTCTT-GGAAAATTGAAGTCAT
* * * *
8702 GTCCATCACATTAGGGCACGATGTTCTCGGAATTTCAAAATTGAAGGACACTTTGCAAGGTTTTA
127 GTCCAACACATTAGGACACGATGTTCTCGGAATTTCAAAATTGAAGGACACTTTGAAAAGTTTTA
* * * *
8767 AAAATGTTATTCGATCGCGCGAATTATACGAAAAATCACACCTTAACACGTTAGGGCATAATTTT
192 AAAAGGATATTCGATCGCACGAATTATACGAAAAATCACACC-CAACACGTTAGGGCATAATTTT
* * * * *
8832 TTGAAATTTTTACACGAAAGGATGTTGCCTCGATTTT-G-AAATTATTT
256 TAGAAACTTTCACACGAAAGGATATTACCTCG-TTTTAGTAAATTATTT
8879 TGTATGTATT
Statistics
Matches: 260, Mismatches: 36, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
319 9 0.03
321 3 0.01
322 140 0.54
323 82 0.32
324 26 0.10
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (320 bp):
TTGAAATCTCGAATGAAGTTTAAAATACGATCCTTCGCACATAACTTATTTCACGTGATTTTAAA
AAACATCAAATTTGAGAAAAAACACCCGTGTGTTTCGAATTTCTTGGAAAATTGAAGTCATGTCC
AACACATTAGGACACGATGTTCTCGGAATTTCAAAATTGAAGGACACTTTGAAAAGTTTTAAAAA
GGATATTCGATCGCACGAATTATACGAAAAATCACACCCAACACGTTAGGGCATAATTTTTAGAA
ACTTTCACACGAAAGGATATTACCTCGTTTTAGTAAATTATTTGAATATTTTTTGAGGAC
Found at i:9268 original size:30 final size:30
Alignment explanation
Indices: 9143--9653 Score: 283
Period size: 30 Copynumber: 17.3 Consensus size: 30
9133 AAAGGGAAAA
* *
9143 AAGGGTCAAAA-ATGAATTTTTG-AAGAATTT
1 AAGGGTCAAAATAT-AATTTTGGAAAG-GTTT
* * *
9173 -AGGGTTAAAACATAATTTTGGAAAAGTTT
1 AAGGGTCAAAATATAATTTTGGAAAGGTTT
* * *
9202 AGGGGTCAAAATATATTTTTGGGAAA-ATTT
1 AAGGGTCAAAATATAATTTT-GGAAAGGTTT
*
9232 --GGGTCAAAATATGATTTTGGAAAGGTTT
1 AAGGGTCAAAATATAATTTTGGAAAGGTTT
* ** *
9260 AAGGGTCAATATGCAATTTTGTAAAGGTTT
1 AAGGGTCAAAATATAATTTTGGAAAGGTTT
* * **
9290 AGGGGTCAATATGCAATTTTGGAAAGGTTT
1 AAGGGTCAAAATATAATTTTGGAAAGGTTT
* *
9320 -AGAGGTCAAAATACAATTTTGGGAAA-ATTT
1 AAG-GGTCAAAATATAATTTT-GGAAAGGTTT
* *
9350 --GGGTCAAAATGTAA-TTTGGAAAAGTTT
1 AAGGGTCAAAATATAATTTTGGAAAGGTTT
*
9377 AAGGGTCAAAACATAATTTTGGGAAA-GTTT
1 AAGGGTCAAAATATAATTTT-GGAAAGGTTT
* *
9407 AGGGGTTAAAATATAATTTTAGGAAA-GTTT
1 AAGGGTCAAAATATAATTTT-GGAAAGGTTT
* * *
9437 -AGAGTTAAAATATAATTTT--AAAGAATTT
1 AAGGGTCAAAATATAATTTTGGAAAG-GTTT
* * *
9465 TAGGTGTCAAAATGTAATTATAGGAAA-GTTT
1 AAGG-GTCAAAATATAATT-TTGGAAAGGTTT
* * *
9496 -AGGGAT-AAAACATTATTTTAGG-AAGTTTT
1 AAGGG-TCAAAATATAATTTT-GGAAAGGTTT
* * * * *
9525 AAGGGTTAAAATGTAATTATGAAAAAGTTT
1 AAGGGTCAAAATATAATTTTGGAAAGGTTT
* * *
9555 AAAGGTTAAAATATAATTTTGGAAAAGTTTT
1 AAGGGTCAAAATATAATTTTGG-AAAGGTTT
** * * **
9586 TTGGGTTAAAATATAATTTTAGAAAAATTTT
1 AAGGGTCAAAATATAATTTT-GGAAAGGTTT
* *
9617 GAA--GTCAAAATATAATTTTGGGATGGTTT
1 -AAGGGTCAAAATATAATTTTGGAAAGGTTT
*
9646 AGGGGTCA
1 AAGGGTCA
9654 TTTAATACAA
Statistics
Matches: 377, Mismatches: 72, Indels: 64
0.73 0.14 0.12
Matches are distributed among these distances:
26 8 0.02
27 11 0.03
28 37 0.10
29 73 0.19
30 195 0.52
31 49 0.13
32 1 0.00
33 3 0.01
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
AAGGGTCAAAATATAATTTTGGAAAGGTTT
Found at i:9332 original size:118 final size:116
Alignment explanation
Indices: 9186--9653 Score: 346
Period size: 118 Copynumber: 3.9 Consensus size: 116
9176 GTTAAAACAT
* * *
9186 AATTTTGGAAAAGTTTAGGGGTCAAAATATATTTTTGGGAAAATTTGGGTCAAAATATGATTTTG
1 AATTTTGG-AAAGTTTAGAGGTCAAAATATAATTTTGGGAAAATTTGGGTCAAAATAT-AATTTG
* * ** * * *
9251 GAAAGGTTTAAGGGTCAATATGCAATTTT-GTAAAGGTTTAGGGGTCAATATGC
64 GAAAAGTTTAAGGGTCAAAACACAATTTTGGGAAA-GTTTAGGGGTCAAAATAC
* *
9304 AATTTTGGAAAGGTTTAGAGGTCAAAATACAATTTTGGGAAAATTTGGGTCAAAATGTAATTTGG
1 AATTTTGGAAA-GTTTAGAGGTCAAAATATAATTTTGGGAAAATTTGGGTCAAAATATAATTTGG
* * *
9369 AAAAGTTTAAGGGTCAAAACATAATTTTGGGAAAGTTTAGGGGTTAAAATAT
65 AAAAGTTTAAGGGTCAAAACACAATTTTGGGAAAGTTTAGGGGTCAAAATAC
* * *
9421 AATTTTAGGAAAGTTTAGA-GTTAAAATATAATTTT--AAAGAATTTTAGGTGTCAAAATGTAAT
1 AATTTT-GGAAAGTTTAGAGGTCAAAATATAATTTTGGGAA-AA-TTT-GG-GTCAAAATATAAT
** * * * **
9483 TATAGG-AAAGTTT-AGGGAT-AAAACATTATTTTAGG-AAGTTTTAAGGGTTAAAATGT
61 T-T-GGAAAAGTTTAAGGG-TCAAAACACAATTTTGGGAAAG-TTTAGGGGTCAAAATAC
* * * * *
9539 AATTATGAAAAAGTTTAAAGGTTAAAATATAATTTT-GGAAAAGTTTTTTGGGTTAAAATATAAT
1 AATTTTG-GAAAGTTTAGAGGTCAAAATATAATTTTGGGAAAA----TTTGGGTCAAAATATAA-
* * * * **
9603 TTTAGAAAAATTTTGAA--GTCAAAATATAATTTTGGGATGGTTTAGGGGTCA
60 TTT-GGAAAAGTTT-AAGGGTCAAAACACAATTTTGGGAAAGTTTAGGGGTCA
9654 TTTAATACAA
Statistics
Matches: 290, Mismatches: 37, Indels: 43
0.78 0.10 0.12
Matches are distributed among these distances:
114 2 0.01
115 2 0.01
116 17 0.06
117 65 0.22
118 120 0.41
119 27 0.09
120 18 0.06
121 33 0.11
122 5 0.02
123 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (116 bp):
AATTTTGGAAAGTTTAGAGGTCAAAATATAATTTTGGGAAAATTTGGGTCAAAATATAATTTGGA
AAAGTTTAAGGGTCAAAACACAATTTTGGGAAAGTTTAGGGGTCAAAATAC
Found at i:9452 original size:59 final size:58
Alignment explanation
Indices: 9170--9653 Score: 304
Period size: 59 Copynumber: 8.2 Consensus size: 58
9160 TTTTGAAGAA
* * * * *
9170 TTTA-GGGTTAAAACATAATTTTGGAAAAGTTTAGGGGTCAAAATATATTTTTGGGAAAA
1 TTTAGGGGTCAAAATATAATTTTGG-AAAGTTTA-GAGTCAAAATATAATTTTGGGAAAG
* * * ** *
9229 TTT--GGGTCAAAATATGATTTTGGAAAGGTTTAAGGGTCAATATGCAATTTT-GTAAAGG
1 TTTAGGGGTCAAAATATAATTTTGGAAA-GTTT-AGAGTCAAAATATAATTTTGGGAAA-G
* ** * *
9287 TTTAGGGGTCAATATGCAATTTTGGAAAGGTTTAGAGGTCAAAATACAATTTTGGGAAAA
1 TTTAGGGGTCAAAATATAATTTTGGAAA-GTTTAGA-GTCAAAATATAATTTTGGGAAAG
* * *
9347 TTT--GGGTCAAAATGTAA-TTTGGAAAAGTTTAAGGGTCAAAACATAATTTTGGGAAAG
1 TTTAGGGGTCAAAATATAATTTTGG-AAAGTTT-AGAGTCAAAATATAATTTTGGGAAAG
* * ** *
9404 TTTAGGGGTTAAAATATAATTTTAGGAAAGTTTAGAGTTAAAATATAATTTT-AAAGAAT
1 TTTAGGGGTCAAAATATAATTTT-GGAAAGTTTAGAGTCAAAATATAATTTTGGGA-AAG
* * * * * * *
9463 TTTAGGTGTCAAAATGTAATTATAGGAAAGTTTAGGGAT-AAAACATTATTTTAGG-AAG
1 TTTAGGGGTCAAAATATAATT-TTGGAAAGTTTAGAG-TCAAAATATAATTTTGGGAAAG
* * * * * * * *
9521 TTTTAAGGGTTAAAATGTAATTATGAAAAAGTTTAAAGGTTAAAATATAATTTTGGAAAAG
1 -TTTAGGGGTCAAAATATAATTTTG-GAAAGTTTAGA-GTCAAAATATAATTTTGGGAAAG
** * * * * **
9582 TTTTTTGGGTTAAAATATAATTTTAGAAAAATTTTGAAGTCAAAATATAATTTTGGGATGG
1 -TTTAGGGGTCAAAATATAATTTT-GGAAAGTTTAG-AGTCAAAATATAATTTTGGGAAAG
9643 TTTAGGGGTCA
1 TTTAGGGGTCA
9654 TTTAATACAA
Statistics
Matches: 333, Mismatches: 68, Indels: 47
0.74 0.15 0.10
Matches are distributed among these distances:
57 39 0.12
58 59 0.18
59 104 0.31
60 74 0.22
61 55 0.17
62 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (58 bp):
TTTAGGGGTCAAAATATAATTTTGGAAAGTTTAGAGTCAAAATATAATTTTGGGAAAG
Found at i:11260 original size:24 final size:21
Alignment explanation
Indices: 11204--11267 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 21
11194 CTTGGATTCT
11204 TTTAAATTTAAATTTAAAGTA
1 TTTAAATTTAAATTTAAAGTA
11225 -TTAGACATTTTAAATTTTAAAGTAAA
1 TTTA-A-A-TTTAAA-TTTAAAGT--A
11251 TTTAAATTTAAAATTTA
1 TTTAAATTT-AAATTTA
11268 TTTATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
20 3 0.09
21 1 0.03
22 1 0.03
23 6 0.17
24 15 0.43
25 4 0.11
26 2 0.06
27 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTAAATTTAAATTTAAAGTA
Found at i:22462 original size:37 final size:37
Alignment explanation
Indices: 22409--22481 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
22399 CGTTCTCTCC
*
22409 AGTGTCTTTTCATTCTTTGGTTCCATTCCCTCTTTCG
1 AGTGTCTTTTCATTCTTAGGTTCCATTCCCTCTTTCG
* *
22446 AGTGTGTTTTCGTTCTTAGGTTCCATTCCCTCTTTC
1 AGTGTCTTTTCATTCTTAGGTTCCATTCCCTCTTTC
22482 CCTATAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.08, C:0.26, G:0.15, T:0.51
Consensus pattern (37 bp):
AGTGTCTTTTCATTCTTAGGTTCCATTCCCTCTTTCG
Found at i:27127 original size:19 final size:20
Alignment explanation
Indices: 27099--27144 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
27089 TTTTGTTACG
27099 ATAA-TTTTTTACAAATTTT
1 ATAATTTTTTTACAAATTTT
**
27118 AT-ATTTTTTTACATTTTTT
1 ATAATTTTTTTACAAATTTT
27137 ATAATTTT
1 ATAATTTT
27145 ATTATGACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
ATAATTTTTTTACAAATTTT
Found at i:30971 original size:3 final size:3
Alignment explanation
Indices: 30915--30953 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
30905 TTTTTCATAT
*
30915 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30954 TGCCCCTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:31151 original size:24 final size:24
Alignment explanation
Indices: 31121--31183 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
31111 AGAAATAATC
31121 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
*
31145 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
31169 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
31184 TATTAGTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:34856 original size:12 final size:12
Alignment explanation
Indices: 34839--34866 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34829 TCTAAAAAGT
34839 TAAAAAAATATA
1 TAAAAAAATATA
34851 TAAAAAAATATA
1 TAAAAAAATATA
34863 TAAA
1 TAAA
34867 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAAAAAATATA
Done.