Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011817.1 Kokia drynarioides strain JFW-HI SEQ_126812, 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: 39727
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:2453 original size:2 final size:2
Alignment explanation
Indices: 2446--2472 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2436 CTCAGACATC
2446 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2473 CCTCCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:7443 original size:20 final size:21
Alignment explanation
Indices: 7418--7460 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
7408 ATTCAAGGGA
* *
7418 TGAAATATATTT-TTTATAAT
1 TGAAATAAATTTCTGTATAAT
7438 TGAAATAAATTTCTGTATAAT
1 TGAAATAAATTTCTGTATAAT
7459 TG
1 TG
7461 TAAAACGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (21 bp):
TGAAATAAATTTCTGTATAAT
Found at i:13931 original size:25 final size:24
Alignment explanation
Indices: 13903--13976 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
13893 AAAAAGAAAA
13903 AAAATATATTAAAATAAAAAAAATT
1 AAAATAT-TTAAAATAAAAAAAATT
* * *
13928 AAAAGTATTTAAATTTAAAAATATT
1 AAAA-TATTTAAAATAAAAAAAATT
*
13953 -AAA-ATTTAAAATATATAAAAATT
1 AAAATATTTAAAATA-AAAAAAATT
13976 A
1 A
13977 GTATTAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
22 8 0.21
23 7 0.18
24 3 0.08
25 18 0.46
26 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (24 bp):
AAAATATTTAAAATAAAAAAAATT
Found at i:13973 original size:17 final size:16
Alignment explanation
Indices: 13913--13996 Score: 69
Period size: 16 Copynumber: 5.0 Consensus size: 16
13903 AAAATATATT
* *
13913 AAAATAAAAAAAATTA
1 AAAATATAAAAATTTA
* **
13929 AAAGTATTTAAATTTA
1 AAAATATAAAAATTTA
*
13945 AAAATATTAAAATTTA
1 AAAATATAAAAATTTA
13961 AAATATATAAAAATTAGTA
1 AAA-ATATAAAAATT--TA
*
13980 TTAAATATAAAAATTTA
1 -AAAATATAAAAATTTA
13997 TAAGATTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
16 28 0.51
17 12 0.22
19 13 0.24
20 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATATAAAAATTTA
Found at i:14106 original size:27 final size:27
Alignment explanation
Indices: 14038--14105 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
14028 TCACATCGTG
** *
14038 ATAAAAATATTAAAATCTATAAAAATT
1 ATAAAAATAAGAAAATATATAAAAATT
*
14065 ATAAAAATAAGAAAATATAT-AAATTT
1 ATAAAAATAAGAAAATATATAAAAATT
14091 AT-AAAATATAGAAAA
1 ATAAAAATA-AGAAAA
14106 AAATTGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.17
26 13 0.36
27 17 0.47
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (27 bp):
ATAAAAATAAGAAAATATATAAAAATT
Found at i:15025 original size:4 final size:4
Alignment explanation
Indices: 15018--15049 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
15008 TGTTGGTTGG
15018 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
15050 GTTTTTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:15704 original size:102 final size:101
Alignment explanation
Indices: 15524--15793 Score: 378
Period size: 102 Copynumber: 2.6 Consensus size: 101
15514 ACGGATTATT
* * * *
15524 CGTTGGTTAATCCAACTAGAGCTTGACTCACATATCGTGGTTTATCTGCTAGGCACTAGGTGTCA
1 CGTTGGTTAATCCAACTAGAGC-TGGCTCACATATCGCGGTTTATCCGCTAGGCACTAGGTGCCA
15589 TAATCGTCAGTTTATCCGACTAGCGCTAGGCACAAAC
65 TAATCGTCAGTTTATCCGACTAGCGCTAGGCACAAAC
* * *
15626 CGTTGGTTAATCCAACCAGAGCTGGTCTCACATATCGCGGTTTATCCGTTAGGCACTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTGG-CTCACATATCGCGGTTTATCCGCTAGGCACTAGGTGCCA
* **
15691 TAATCGTCGGTTTATCCGACTAGCGCTAGGTGCAAAC
65 TAATCGTCAGTTTATCCGACTAGCGCTAGGCACAAAC
* * * * *
15728 CATTGGATAATCCAACTAGAGCTGAGCTCACATATCGCGGTATATCCGCAAGGCACTTGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTG-GCTCACATATCGCGGTTTATCCGCTAGGCACTAGGTGCCA
15793 T
65 T
15794 GAATTGACGG
Statistics
Matches: 149, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
101 2 0.01
102 146 0.98
103 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (101 bp):
CGTTGGTTAATCCAACTAGAGCTGGCTCACATATCGCGGTTTATCCGCTAGGCACTAGGTGCCAT
AATCGTCAGTTTATCCGACTAGCGCTAGGCACAAAC
Found at i:15723 original size:35 final size:36
Alignment explanation
Indices: 15552--15724 Score: 109
Period size: 35 Copynumber: 5.1 Consensus size: 36
15542 GAGCTTGACT
* *
15552 CACAT-ATCGT-GGTTTATCTG-CTAGGCACTAGGTG
1 CACATAATCGTCGGTTTATCCGACTA-GCGCTAGGTG
* *
15586 -TCATAATCGTCAGTTTATCCGACTAGCGCTA-G-G
1 CACATAATCGTCGGTTTATCCGACTAGCGCTAGGTG
* * * * * * *
15619 CACA-AACCGTTGGTTAATCCAACCAGAGCT-GGTCT
1 CACATAATCGTCGGTTTATCCGACTAGCGCTAGGT-G
* * *
15654 CACAT-ATCG-CGGTTTATCCG-TTAGGCACTGGGTG
1 CACATAATCGTCGGTTTATCCGACTA-GCGCTAGGTG
15688 C-CATAATCGTCGGTTTATCCGACTAGCGCTAGGTG
1 CACATAATCGTCGGTTTATCCGACTAGCGCTAGGTG
15723 CA
1 CA
15725 AACCATTGGA
Statistics
Matches: 100, Mismatches: 25, Indels: 26
0.66 0.17 0.17
Matches are distributed among these distances:
33 28 0.28
34 24 0.24
35 43 0.43
36 5 0.05
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (36 bp):
CACATAATCGTCGGTTTATCCGACTAGCGCTAGGTG
Found at i:17376 original size:30 final size:32
Alignment explanation
Indices: 17324--17390 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
17314 TTTTTTTAGC
*
17324 TTTT-AGGGGCTTAAAATGTTTTTTTATCAAT
1 TTTTAAGGGACTTAAAATGTTTTTTTATCAAT
*
17355 TTTTAAGGGACTT-AAAT-TTTTTTTTTCAAT
1 TTTTAAGGGACTTAAAATGTTTTTTTATCAAT
17385 TTTTAA
1 TTTTAA
17391 AGAACCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 18 0.55
31 8 0.24
32 7 0.21
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (32 bp):
TTTTAAGGGACTTAAAATGTTTTTTTATCAAT
Found at i:17378 original size:32 final size:30
Alignment explanation
Indices: 17324--17390 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
17314 TTTTTTTAGC
*
17324 TTTT-AGGGGCTTAAAATGTTTTTTTATCAAT
1 TTTTAAGGGACTT-AAATGTTTTTTT-TCAAT
*
17355 TTTTAAGGGACTTAAATTTTTTTTTTCAAT
1 TTTTAAGGGACTTAAATGTTTTTTTTCAAT
17385 TTTTAA
1 TTTTAA
17391 AGAACCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 11 0.33
31 15 0.45
32 7 0.21
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (30 bp):
TTTTAAGGGACTTAAATGTTTTTTTTCAAT
Found at i:20945 original size:80 final size:80
Alignment explanation
Indices: 20860--21020 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
20850 TTATTGTTCG
*
20860 ACATGTTCTTATTGTCAGTGTTTGATTATTACACCAAAACATCACTTACAAGTTAATATTTTATC
1 ACATGTTCTTATTGTCAGTGTTTGATTACTACACCAAAACATCACTTACAAGTTAATATTTTATC
20925 CAAAGATGAAATATT
66 CAAAGATGAAATATT
20940 ACATGTTCTTATTGTCAGTGTTTGATTACTACACCAAAACATCACTTACAAGTTAATATTTTATC
1 ACATGTTCTTATTGTCAGTGTTTGATTACTACACCAAAACATCACTTACAAGTTAATATTTTATC
*
21005 CAAAGATGAATTATT
66 CAAAGATGAAATATT
21020 A
1 A
21021 ATGGAGTGTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (80 bp):
ACATGTTCTTATTGTCAGTGTTTGATTACTACACCAAAACATCACTTACAAGTTAATATTTTATC
CAAAGATGAAATATT
Found at i:26526 original size:23 final size:23
Alignment explanation
Indices: 26499--26545 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
26489 ATAAACAAAC
*
26499 GGTTCATGAATAGTTCATCCAAT
1 GGTTCACGAATAGTTCATCCAAT
26522 GGTTCACGAATAGTTCATCCAAT
1 GGTTCACGAATAGTTCATCCAAT
26545 G
1 G
26546 TTTTGTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (23 bp):
GGTTCACGAATAGTTCATCCAAT
Found at i:30491 original size:16 final size:16
Alignment explanation
Indices: 30470--30519 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
30460 CGTTACATAT
30470 AATAAAAATATTAAAA
1 AATAAAAATATTAAAA
* *
30486 AATAAAAACAATAAAA
1 AATAAAAATATTAAAA
30502 ATTATAAAAATTATTAAA
1 A--ATAAAAA-TATTAAA
30520 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 15 0.56
18 7 0.26
19 5 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAAATATTAAAA
Found at i:30534 original size:30 final size:30
Alignment explanation
Indices: 30498--30562 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
30488 TAAAAACAAT
30498 AAAAATTATAAAAAT-TATTAAATTTTAATA
1 AAAAATTATAAAAATAT-TTAAATTTTAATA
*
30528 AAAAATTATAAAAATATTTAAATTTTATTA
1 AAAAATTATAAAAATATTTAAATTTTAATA
30558 AAAAA
1 AAAAA
30563 GAGAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAATTATAAAAATATTTAAATTTTAATA
Found at i:30542 original size:9 final size:9
Alignment explanation
Indices: 30471--30542 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
30461 GTTACATATA
30471 ATAAAAA-T
1 ATAAAAATT
30479 ATTAAAAA--
1 A-TAAAAATT
**
30487 ATAAAAACA
1 ATAAAAATT
30496 ATAAAAATT
1 ATAAAAATT
30505 ATAAAAATT
1 ATAAAAATT
**
30514 ATTAAATTTT
1 A-TAAAAATT
30524 AATAAAAAATT
1 -AT-AAAAATT
30535 ATAAAAAT
1 ATAAAAAT
30543 ATTTAAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
7 6 0.12
8 2 0.04
9 29 0.56
10 9 0.17
11 6 0.12
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:30571 original size:30 final size:29
Alignment explanation
Indices: 30498--30577 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
30488 TAAAAACAAT
* *
30498 AAAAATTATAAAAATTATTAAATTTTAATA
1 AAAAATGA-AAAAAATATTAAATTTTAATA
* * *
30528 AAAAATTATAAAAATATTTAAATTTTATTA
1 AAAAATGAAAAAAATA-TTAAATTTTAATA
30558 AAAAA-GAGAAAAAAT-TTAAA
1 AAAAATGA-AAAAAATATTAAA
30578 ATATATAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 5 0.12
29 7 0.16
30 31 0.72
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATGAAAAAAATATTAAATTTTAATA
Found at i:30897 original size:22 final size:22
Alignment explanation
Indices: 30869--30914 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
30859 TTTTTTTTTA
30869 TTTTTATAAAAATTTACAATTT
1 TTTTTATAAAAATTTACAATTT
***
30891 TTTTTATAATTTTTTACAATTT
1 TTTTTATAAAAATTTACAATTT
30913 TT
1 TT
30915 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATAAAAATTTACAATTT
Found at i:30948 original size:29 final size:29
Alignment explanation
Indices: 30894--30968 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 29
30884 ACAATTTTTT
*
30894 TTATAATTTTTTACA-ATTTTTATAAAAAAAA
1 TTAT-ATTTTTTA-ATATATTTAT-AAAAAAA
* *
30925 TTCTATTTTTTAATATATTT-TAAATAAA
1 TTATATTTTTTAATATATTTATAAAAAAA
30953 TTATATCTTTTTAATA
1 TTATAT-TTTTTAATA
30969 AAATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 11 0.29
29 11 0.29
30 13 0.34
31 3 0.08
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
TTATATTTTTTAATATATTTATAAAAAAA
Found at i:30983 original size:19 final size:20
Alignment explanation
Indices: 30961--31003 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
30951 AATTATATCT
30961 TTTTAATAAAATTTA-ATAA
1 TTTTAATAAAATTTATATAA
* *
30980 TTTT-ATAAATTTTATTTAA
1 TTTTAATAAAATTTATATAA
30999 TTTTA
1 TTTTA
31004 TTTTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAATAAAATTTATATAA
Found at i:30986 original size:29 final size:29
Alignment explanation
Indices: 30922--30976 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
30912 TTTATAAAAA
* * *
30922 AAATTCTAT-TTTTTAATATATTTTAAAT
1 AAATTATATCTTTTTAATAAAATTTAAAT
30950 AAATTATATCTTTTTAATAAAATTTAA
1 AAATTATATCTTTTTAATAAAATTTAA
30977 TAATTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATTATATCTTTTTAATAAAATTTAAAT
Found at i:31331 original size:19 final size:19
Alignment explanation
Indices: 31307--31351 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
31297 GTTAAAATAC
**
31307 AAATTAGTTTAAATTTAAA
1 AAATTAGTTTAAATAAAAA
*
31326 AAATTAGTTTAGATAAAAA
1 AAATTAGTTTAAATAAAAA
31345 AAATTAG
1 AAATTAG
31352 AGTCATTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (19 bp):
AAATTAGTTTAAATAAAAA
Found at i:36885 original size:20 final size:19
Alignment explanation
Indices: 36860--36897 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
36850 AATCAGCAAA
36860 GGAAAGGACAAGGAAGAAAT
1 GGAAAGGA-AAGGAAGAAAT
*
36880 GGAAAGGAAAGGGAGAAA
1 GGAAAGGAAAGGAAGAAA
36898 GTGAGTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.39, T:0.03
Consensus pattern (19 bp):
GGAAAGGAAAGGAAGAAAT
Found at i:39394 original size:24 final size:24
Alignment explanation
Indices: 39331--39385 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
39321 ACTCTGTCTA
* * **
39331 GGCTCATAAGAGTTAACCATTCTG
1 GGCTCGTAAGAGCTAATTATTCTG
39355 GGCTCGTAAGAGCTAATTATTCTG
1 GGCTCGTAAGAGCTAATTATTCTG
39379 GGCTCGT
1 GGCTCGT
39386 GTGGGCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAATTATTCTG
Done.