Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002356.1 Kokia drynarioides strain JFW-HI SEQ_114424, 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: 41568
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:3414 original size:31 final size:30
Alignment explanation
Indices: 3344--3400 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3334 TTTAGGAGAC
*
3344 GAAATTAAATTATAATTTTTATAATTTAAA
1 GAAATTAAAATATAATTTTTATAATTTAAA
3374 GAAATTAAAATATAATTTATT-TAATTT
1 GAAATTAAAATATAATTT-TTATAATTT
3401 TAAAAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
GAAATTAAAATATAATTTTTATAATTTAAA
Found at i:13713 original size:158 final size:158
Alignment explanation
Indices: 13425--13747 Score: 418
Period size: 158 Copynumber: 2.0 Consensus size: 158
13415 TTTTCTGTAT
* *
13425 CATGTAGTGCTCACATGAGCCATGAAATGGGTCTGCTCACATGAGCTATGGGTCGAGATGTTAAG
1 CATGTAATGCTCACATGAGCCATGAAATGGGTCTGCTCACATGAGCTATGGGTCAAGATGTTAAG
* * * *
13490 CTACACAATACTACTCATACGAGTTGTGGAGAATCCACAACATATGTCGGATCTCAGCCATCAGT
66 CTACACAATACTACTCACACGAGTTGTGGAGAATCCACAACATATGCCAGATCTCAACCATCAGT
* * * *
13555 AGGACATTTAGGACCAGCACTCATATAA
131 AGGACATCTAAGACCAACACCCATATAA
* *
13583 CATGTAATGCTCACATGAG-C-TGTAAAGTGGGTCTGCTCACATGAGTTGTGGGTCAAGATGTTA
1 CATGTAATGCTCACATGAGCCATG-AAA-TGGGTCTGCTCACATGAGCTATGGGTCAAGATGTTA
* * * * * **
13646 AGCTACTCGATGCTGCTTACACGAGCTT-TGGAGAATCCGTAACATATGCCAGATCTCAACCATC
64 AGCTACACAATACTACTCACACGAG-TTGTGGAGAATCCACAACATATGCCAGATCTCAACCATC
*
13710 AGTAGGTCATCTAAGACCAACACCCATATAA
128 AGTAGGACATCTAAGACCAACACCCATATAA
13741 CATGTAA
1 CATGTAA
13748 ATCCCAAAAT
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
156 2 0.01
157 4 0.03
158 134 0.94
159 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (158 bp):
CATGTAATGCTCACATGAGCCATGAAATGGGTCTGCTCACATGAGCTATGGGTCAAGATGTTAAG
CTACACAATACTACTCACACGAGTTGTGGAGAATCCACAACATATGCCAGATCTCAACCATCAGT
AGGACATCTAAGACCAACACCCATATAA
Found at i:14613 original size:12 final size:13
Alignment explanation
Indices: 14596--14624 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
14586 AAAGTCAAAA
14596 TTTTCTTTTT-CT
1 TTTTCTTTTTCCT
14608 TTTTCTTTTTCCT
1 TTTTCTTTTTCCT
14621 TTTT
1 TTTT
14625 AATTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCCT
Found at i:15122 original size:15 final size:16
Alignment explanation
Indices: 15085--15126 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
15075 ACAAATGTGA
*
15085 AAAATATATATTTTTT
1 AAAATTTATATTTTTT
*
15101 ATTAATTTATA-TTTTT
1 A-AAATTTATATTTTTT
15117 AAAATTTATA
1 AAAATTTATA
15127 AATTTATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAAATTTATATTTTTT
Found at i:23195 original size:29 final size:30
Alignment explanation
Indices: 23170--23242 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 30
23160 ATTAAAATTA
23170 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
* *
23201 TTTAATAATTTTATATTT-TAAAAAATGAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
23230 TTTAATAATTTTA
1 TTTAATAATTTTA
23243 AAATCATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 22 0.55
30 5 0.12
31 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:26304 original size:25 final size:24
Alignment explanation
Indices: 26248--26300 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
26238 TTGACAAAAT
* *
26248 TAAATAGAACAATTAAGCAGATAAG
1 TAAATACAAAAATTAAGCA-ATAAG
26273 TAAATACAAAAATTAAGC-ATAAG
1 TAAATACAAAAATTAAGCAATAAG
26296 ATAAA
1 -TAAA
26301 ATACGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 16 0.64
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (24 bp):
TAAATACAAAAATTAAGCAATAAG
Found at i:26449 original size:29 final size:30
Alignment explanation
Indices: 26414--26732 Score: 145
Period size: 29 Copynumber: 11.1 Consensus size: 30
26404 GAAAAAAACG
26414 GGGTCAAAAATGAAGTTTT-GAAGAA-TTTA
1 GGGTCAAAAATGAAGTTTTGGAA-AAGTTTA
26443 GGGTCAAAACAT-AA-TTTTGGAAAAGTTTA
1 GGGTCAAAA-ATGAAGTTTTGGAAAAGTTTA
*
26472 GGGT-AAAAATGTAGTTTTGGAAAAGTTTA
1 GGGTCAAAAATGAAGTTTTGGAAAAGTTTA
** * *
26501 GGGTC-AAAATGTGGCTTT-GAGAAAGTTAA
1 GGGTCAAAAATGAAGTTTTGGA-AAAGTTTA
* * * *
26530 GGG-CTAAAATG-TGATTTTGAAAAAGTGTGA
1 GGGTCAAAAATGAAG-TTTTGGAAAAGT-TTA
*
26560 GGGT------T-AA-TTTTGGAAAAGTTTG
1 GGGTCAAAAATGAAGTTTTGGAAAAGTTTA
* *
26582 GGGTC-AAAATG-TGATTTTGGAAAAGTTTG
1 GGGTCAAAAATGAAG-TTTTGGAAAAGTTTA
*
26611 GGAGTTAAAAATGTAA-TTTTAGG-AAAGTTTA
1 GG-GTCAAAAATG-AAGTTTT-GGAAAAGTTTA
* * *
26642 GGATTAAAATATG--GTTTTGGGAAAGTTT-
1 GGGTCAAAA-ATGAAGTTTTGGAAAAGTTTA
* *
26670 GAGGTCAAAACGTG-A-TTTTGAAAAAGTTTGA
1 G-GGTCAAAA-ATGAAGTTTTGGAAAAGTTT-A
*
26701 GGGTC-AAAATG-TGATTTTGGAAAAGTTTA
1 GGGTCAAAAATGAAG-TTTTGGAAAAGTTTA
26730 GGG
1 GGG
26733 GTTTAAACAT
Statistics
Matches: 229, Mismatches: 26, Indels: 70
0.70 0.08 0.22
Matches are distributed among these distances:
22 5 0.02
23 11 0.05
25 1 0.00
27 3 0.01
28 20 0.09
29 131 0.57
30 33 0.14
31 23 0.10
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
GGGTCAAAAATGAAGTTTTGGAAAAGTTTA
Found at i:26504 original size:58 final size:57
Alignment explanation
Indices: 26414--26797 Score: 215
Period size: 58 Copynumber: 6.6 Consensus size: 57
26404 GAAAAAAACG
*
26414 GGGTCAAAAATGAAGTTTT-GAAGAA-TTTAGGGTCAAAACATAATTTTGGAAAAGTTTA
1 GGGT-AAAAATG-TGTTTTGGAA-AAGTTTAGGGTCAAAACATAATTTTGGAAAAGTTTA
** *** *
26472 GGGTAAAAATGTAGTTTTGGAAAAGTTTAGGGTCAAAATGTGGCTTT-GAGAAAGTTAA
1 GGGTAAAAATGT-GTTTTGGAAAAGTTTAGGGTCAAAACATAATTTTGGA-AAAGTTTA
* * *
26530 GGGCT-AAAATGTGATTTTGAAAAAGTGTGAGGGT-------TAATTTTGGAAAAGTTTG
1 GGG-TAAAAATGTG-TTTTGGAAAAGT-TTAGGGTCAAAACATAATTTTGGAAAAGTTTA
* * *
26582 GGGTCAAAATGTGATTTTGGAAAAGTTTGGGAGTTAAAA-ATGTAATTTTAGG-AAAGTTTA
1 GGGTAAAAATGTG-TTTTGGAAAAGTTTAGG-GTCAAAACA--TAATTTT-GGAAAAGTTTA
* * * * *
26642 GGATTAAAATATG-GTTTTGGGAAAGTTT-GAGGTCAAAACGTGATTTTGAAAAAGTTTGA
1 GG-GTAAAA-ATGTGTTTTGGAAAAGTTTAG-GGTCAAAACATAATTTTGGAAAAGTTT-A
* ** * *
26701 GGGTCAAAATGTGATTTTGGAAAAGTTTAGGGGTTTAAACATAATTTTAGAGAAG-TTA
1 GGGTAAAAATGTG-TTTTGGAAAAGTTTA-GGGTCAAAACATAATTTTGGAAAAGTTTA
* * * * *
26759 GAGGTTAAAATATAATTTTGGAAAGGTTTAGGGTTAAAA
1 G-GGTAAAAATGT-GTTTTGGAAAAGTTTAGGGTCAAAA
26798 TGTGATTTTG
Statistics
Matches: 255, Mismatches: 40, Indels: 62
0.71 0.11 0.17
Matches are distributed among these distances:
51 4 0.02
52 35 0.14
53 2 0.01
57 21 0.08
58 80 0.31
59 55 0.22
60 47 0.18
61 8 0.03
62 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (57 bp):
GGGTAAAAATGTGTTTTGGAAAAGTTTAGGGTCAAAACATAATTTTGGAAAAGTTTA
Found at i:26757 original size:89 final size:86
Alignment explanation
Indices: 26564--26808 Score: 242
Period size: 89 Copynumber: 2.8 Consensus size: 86
26554 GTGTGAGGGT
* * *
26564 TAATTTTGGAAAAGTTTGGGGTCAAAATGTGATTTTGGAAAAGTTTG-GGAGTTAAAAATGTAAT
1 TAATTTT-GAGAAGTTTGAGGTCAAAATGTGATTTTGGAAAAGTTTGAGG-G-TAAAAATGTGAT
*
26628 TTTAGGAAAGTTTAGGATTAAAATA
63 TTT-GGAAAGTTTAGGATTAAAACA
** * * * *
26653 TGGTTTTGGGAAAGTTTGAGGTCAAAACGTGATTTTGAAAAAGTTTGAGGGTCAAAATGTGATTT
1 TAATTTTGAG-AAGTTTGAGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTAAAAATGTGATTT
* *
26718 TGGAAAAGTTTAGGGGTTTAAACA
65 TGG-AAAGTTTA-GGATTAAAACA
* * * * * *
26742 TAATTTTAGAGAAGTTAGAGGTTAAAATATAATTTTGGAAAGGTTT-AGGGTTAAAATGTGATTT
1 TAATTTT-GAGAAGTTTGAGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTAAAAATGTGATTT
26806 TGG
65 TGG
26809 GTAAATAGGG
Statistics
Matches: 128, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
87 2 0.02
88 42 0.33
89 80 0.62
90 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (86 bp):
TAATTTTGAGAAGTTTGAGGTCAAAATGTGATTTTGGAAAAGTTTGAGGGTAAAAATGTGATTTT
GGAAAGTTTAGGATTAAAACA
Found at i:26805 original size:29 final size:29
Alignment explanation
Indices: 26456--26808 Score: 271
Period size: 29 Copynumber: 12.2 Consensus size: 29
26446 TCAAAACATA
*
26456 ATTTTGGAAAAGTTTAGGGTAAAAATGT-
1 ATTTTGGAAAAGTTTAGGGTTAAAATGTG
*
26484 AGTTTTGGAAAAGTTTAGGGTCAAAATGTG
1 A-TTTTGGAAAAGTTTAGGGTTAAAATGTG
** * *
26514 GCTTT-GAGAAAGTTAAGGGCTAAAATGTG
1 ATTTTGGA-AAAGTTTAGGGTTAAAATGTG
* *
26543 ATTTTGAAAAAGTGTGAGGGTT---A----
1 ATTTTGGAAAAGT-TTAGGGTTAAAATGTG
* *
26566 ATTTTGGAAAAGTTTGGGGTCAAAATGTG
1 ATTTTGGAAAAGTTTAGGGTTAAAATGTG
* *
26595 ATTTTGGAAAAGTTTGGGAGTTAAAAATGTA
1 ATTTTGGAAAAGTTTAGG-GTT-AAAATGTG
* *
26626 ATTTTAGG-AAAGTTTAGGATTAAAATATG
1 ATTTT-GGAAAAGTTTAGGGTTAAAATGTG
* * * *
26655 GTTTTGGGAAAGTTT-GAGGTCAAAACGTG
1 ATTTTGGAAAAGTTTAG-GGTTAAAATGTG
* *
26684 ATTTTGAAAAAGTTTGAGGGTCAAAATGTG
1 ATTTTGGAAAAGTTT-AGGGTTAAAATGTG
* ** *
26714 ATTTTGGAAAAGTTTAGGGGTTTAAACATA
1 ATTTTGGAAAAGTTTA-GGGTTAAAATGTG
* * * *
26744 ATTTTAGAGAAG-TTAGAGGTTAAAATATA
1 ATTTTGGAAAAGTTTAG-GGTTAAAATGTG
*
26773 ATTTTGGAAAGGTTTAGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTAGGGTTAAAATGTG
26802 ATTTTGG
1 ATTTTGG
26809 GTAAATAGGG
Statistics
Matches: 258, Mismatches: 45, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
22 5 0.02
23 12 0.05
25 1 0.00
27 1 0.00
28 7 0.03
29 150 0.58
30 58 0.22
31 22 0.09
32 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
ATTTTGGAAAAGTTTAGGGTTAAAATGTG
Found at i:35014 original size:22 final size:22
Alignment explanation
Indices: 34986--35028 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
34976 TAAAACTAAG
34986 TAAGCTAAGAGATTGGAATGGA
1 TAAGCTAAGAGATTGGAATGGA
35008 TAAGCTAAGAGATTGGAATGG
1 TAAGCTAAGAGATTGGAATGG
35029 CTAAAATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.23
Consensus pattern (22 bp):
TAAGCTAAGAGATTGGAATGGA
Done.