Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012106.1 Kokia drynarioides strain JFW-HI SEQ_127105, 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: 19138
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:359 original size:30 final size:28
Alignment explanation
Indices: 308--555 Score: 198
Period size: 29 Copynumber: 8.4 Consensus size: 28
298 CGGATGCACG
* * * *
308 GGGGCAAAATGGTAGTTTTGGAGGGTTC
1 GGGGTAAAATGGGATTTTTGGAAGGTTC
*
336 GGAGTCAAAATTGGGATTTTTGGAA-GTTC
1 GGGGT-AAAA-TGGGATTTTTGGAAGGTTC
* * *
365 GGGGGTAAAATGGTAATTTTTAGAAGGTTA
1 -GGGGTAAAATGG-GATTTTTGGAAGGTTC
395 GGGGTCAAAAATGGGATTTTTGGAA-GTTC
1 GGGGT--AAAATGGGATTTTTGGAAGGTTC
* *
424 GGGGGTAAAATGGTAATTTTTAGAAGGTTC
1 -GGGGTAAAATGG-GATTTTTGGAAGGTTC
* *
454 GGGATAAAAAATGGGATTTTT-GAAAGTTC
1 GGGGT--AAAATGGGATTTTTGGAAGGTTC
* *
483 GGGGGTAAAATGGTAATTTTTAGAAGGGTTC
1 -GGGGTAAAATGG-GATTTTTGGAA-GGTTC
514 GGGGTCAAAGATGGGATTTTTGGAA-GTTC
1 GGGGT-AAA-ATGGGATTTTTGGAAGGTTC
543 GGGGGTAAAATGG
1 -GGGGTAAAATGG
556 TAANNNNNNN
Statistics
Matches: 179, Mismatches: 22, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
28 24 0.13
29 62 0.35
30 59 0.33
31 30 0.17
32 4 0.02
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (28 bp):
GGGGTAAAATGGGATTTTTGGAAGGTTC
Found at i:542 original size:60 final size:59
Alignment explanation
Indices: 306--558 Score: 391
Period size: 59 Copynumber: 4.3 Consensus size: 59
296 TTCGGATGCA
* * * * * *
306 CGGGGGCAAAATGGT-AGTTTTGGAGGGTTCGGAGTCAAAATTGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
364 CGGGGGTAAAATGGTAATTTTTAGAAGGTTAGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
423 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGATAAAAAATGGGATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
482 CGGGGGTAAAATGGTAATTTTTAGAAGGGTTCGGGGTCAAAGATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAA-GGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
542 CGGGGGTAAAATGGTAA
1 CGGGGGTAAAATGGTAA
559 NNNNNNNNNN
Statistics
Matches: 178, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
58 14 0.08
59 118 0.66
60 46 0.26
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:672 original size:29 final size:31
Alignment explanation
Indices: 610--692 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
600 NNNNNNNNNT
610 AAAATGGTAATTTTTAGAAGGTTCGGGGTCA
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCA
* *
641 AAAATGG-GATTTTTGGAA-GTTCGGGGGT--
1 AAAATGGTAATTTTTAGAAGGTTC-GGGGTCA
669 AAAATGGTAATTTTTAGAAGGTTC
1 AAAATGGTAATTTTTAGAAGGTTC
693 AGGGACCTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 7 0.16
29 13 0.29
30 18 0.40
31 7 0.16
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (31 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTCA
Found at i:1633 original size:70 final size:70
Alignment explanation
Indices: 1541--1686 Score: 269
Period size: 71 Copynumber: 2.1 Consensus size: 70
1531 CCCTCTGTTC
1541 TTCTTTTCCCTTTTTTTT-AAAAAAAAAACAACATAGATCTCTTTTGTTTTAAAACATAACTTAA
1 TTCTTTTCCCTTTTTTTTAAAAAAAAAAACAACATAGATCTCTTTTGTTTTAAAACATAACTTAA
1605 ATCCG
66 ATCCG
1610 TNTCTTTTCCCTTTTTTTTAAAAAAAAAAACAACATAGATCTCTTTTGTTTTAAAACATAACTTA
1 T-TCTTTTCCCTTTTTTTTAAAAAAAAAAACAACATAGATCTCTTTTGTTTTAAAACATAACTTA
1675 AATCCG
65 AATCCG
1681 -TCTTTT
1 TTCTTTT
1687 GTTTTTAACT
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
69 7 0.09
70 17 0.23
71 51 0.68
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (70 bp):
TTCTTTTCCCTTTTTTTTAAAAAAAAAAACAACATAGATCTCTTTTGTTTTAAAACATAACTTAA
ATCCG
Found at i:1874 original size:17 final size:19
Alignment explanation
Indices: 1854--1891 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
1844 ATTAATATTT
1854 TTATTATT-TTAA-AAAAA
1 TTATTATTATTAATAAAAA
1871 TTATTATTATTAATAAAAA
1 TTATTATTATTAATAAAAA
1890 TT
1 TT
1892 TTGAAAACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTATTATTAATAAAAA
Found at i:2559 original size:17 final size:18
Alignment explanation
Indices: 2534--2575 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2524 GATCGGGCCT
* *
2534 TTTTAGGTTTAGGG-TTA
1 TTTTGGGTTTAGGGCTGA
*
2551 TTTTGGGTTTGGGGCTGA
1 TTTTGGGTTTAGGGCTGA
2569 TTTTGGG
1 TTTTGGG
2576 CCACTTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (18 bp):
TTTTGGGTTTAGGGCTGA
Found at i:2720 original size:16 final size:17
Alignment explanation
Indices: 2653--2721 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
2643 TTGGACTTTC
*
2653 TAAACTT-AATTTTATAA
1 TAAACTTAAATTTCA-AA
*
2670 TAAATTTAAATTTCAAA
1 TAAACTTAAATTTCAAA
2687 TAAACTTAAATTT-AAA
1 TAAACTTAAATTTCAAA
* *
2703 TAAA-TTCAATTTCCAA
1 TAAACTTAAATTTCAAA
2719 TAA
1 TAA
2722 GTCCAGAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.16
16 12 0.27
17 20 0.44
18 6 0.13
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAACTTAAATTTCAAA
Found at i:2941 original size:30 final size:32
Alignment explanation
Indices: 2907--2982 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 32
2897 TGGGTTAATG
*
2907 ATTTAATATAAATATAAAT-ACATAATT-TTT
1 ATTTAAAATAAATATAAATAACATAATTGTTT
* *
2937 ATTTAACAT--ATATAATTAACATAATTGTTT
1 ATTTAAAATAAATATAAATAACATAATTGTTT
2967 -TTTAAAATATAATATA
1 ATTTAAAATA-AATATA
2983 TTCGAGTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 7 0.18
29 15 0.39
30 11 0.29
32 5 0.13
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTTAAAATAAATATAAATAACATAATTGTTT
Found at i:8295 original size:23 final size:24
Alignment explanation
Indices: 8269--8326 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
8259 AAAATTTTGA
* *
8269 AAAATTAATCCCT-TTAATTTATT
1 AAAATTAATCCCTCATAAGTTATT
8292 AAAATTTAAT-CCTCATAAGTTATT
1 AAAA-TTAATCCCTCATAAGTTATT
*
8316 AAAACTAATCC
1 AAAATTAATCC
8327 AATTGTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.40
Consensus pattern (24 bp):
AAAATTAATCCCTCATAAGTTATT
Found at i:11376 original size:82 final size:82
Alignment explanation
Indices: 11239--11402 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
11229 AAGAATATTG
*
11239 AAGAAAAATCCGATGAAACTCTCACATTAAGTTGTTTTATGACATACTTGATCGAAATGAGATAA
1 AAGAAAAATACGATGAAACTCTCACATTAAGTTGTTTTATGACATACTTGATCGAAATGAGATAA
11304 ACAACCACCATGTTATA
66 ACAACCACCATGTTATA
11321 AAGAAAAATACGATGAAACTCTCACATTAAGTTGTTTTATGACATACTTGATCGAAATGAGATAA
1 AAGAAAAATACGATGAAACTCTCACATTAAGTTGTTTTATGACATACTTGATCGAAATGAGATAA
11386 ACAACCACCATGTTATA
66 ACAACCACCATGTTATA
11403 TTTTATAATT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (82 bp):
AAGAAAAATACGATGAAACTCTCACATTAAGTTGTTTTATGACATACTTGATCGAAATGAGATAA
ACAACCACCATGTTATA
Found at i:15382 original size:17 final size:17
Alignment explanation
Indices: 15362--15401 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
15352 ATAAAATTAT
*
15362 TAAATATTAAAATAAAA
1 TAAATATTAAAAAAAAA
15379 TAAATATTAAAAAAAAA
1 TAAATATTAAAAAAAAA
*
15396 TTAATA
1 TAAATA
15402 ATATGGACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATATTAAAAAAAAA
Done.