Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006466.1 Kokia drynarioides strain JFW-HI SEQ_121049, 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: 67183
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:3910 original size:21 final size:21
Alignment explanation
Indices: 3872--3912 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3862 TTTTCAATTT
* *
3872 TGTCAAACTTGTATTTATTAA
1 TGTCAAAATTGTAATTATTAA
*
3893 TGTCAAAATTTTAATTATTA
1 TGTCAAAATTGTAATTATTA
3913 GTACTATACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
TGTCAAAATTGTAATTATTAA
Found at i:6869 original size:16 final size:15
Alignment explanation
Indices: 6848--6877 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6838 CTCCCTACCC
6848 AAAAGAAAGAGAAAAA
1 AAAAGAAAG-GAAAAA
6864 AAAAGAAAGGAAAA
1 AAAAGAAAGGAAAA
6878 TCCCCATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGGAAAAA
Found at i:16012 original size:28 final size:27
Alignment explanation
Indices: 15876--16040 Score: 84
Period size: 28 Copynumber: 6.1 Consensus size: 27
15866 ATGGAGGGGC
* *
15876 ACCATTAGGAGTTGTACCGTGGGTGGTT
1 ACCATTAGGAGTCGTACCGTGGATGG-T
* * * *
15904 ACCCTTAGGAGCCATACCATGGATGGGT
1 ACCATTAGGAGTCGTACCGTGGAT-GGT
* * * ** * *
15932 ACCTTTAGAAATCACACCGCGGATGGC
1 ACCATTAGGAGTCGTACCGTGGATGGT
* * * *
15959 A-TAGT-GGA-TGGTACCGCGGATGGGT
1 ACCATTAGGAGTCGTACCGTGGAT-GGT
*
15984 ACCTTTAGGAGTCGTACCGTGGATAGGT
1 ACCATTAGGAGTCGTACCGTGGAT-GGT
* **
16012 ACCATTAGGAGTTGTGTCGTGGATGGT
1 ACCATTAGGAGTCGTACCGTGGATGGT
16039 AC
1 AC
16041 TACAGATGAG
Statistics
Matches: 100, Mismatches: 32, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
24 10 0.10
25 5 0.05
26 2 0.02
27 11 0.11
28 70 0.70
29 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (27 bp):
ACCATTAGGAGTCGTACCGTGGATGGT
Found at i:16071 original size:68 final size:68
Alignment explanation
Indices: 15962--16090 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 68
15952 GGATGGCATA
* * * * * *
15962 GTGGATGGTACCGCGGATGGGTACCTTTAGGAGTCGTACCGTGGATAGG-TACCATTAGGAGTTG
1 GTGGATGGTACCACAGATGAGTACCGTTAAGAGTCGTACCGTGAAT-GGTTACCATTAGGAGTTG
16026 TGTC
65 TGTC
* * *
16030 GTGGATGGTACTACAGATGAGTACCGTTAAGAGTTGTACCGTGAATGGTTACCCTTAGGAG
1 GTGGATGGTACCACAGATGAGTACCGTTAAGAGTCGTACCGTGAATGGTTACCATTAGGAG
16091 CCGTACCGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
67 2 0.04
68 49 0.96
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (68 bp):
GTGGATGGTACCACAGATGAGTACCGTTAAGAGTCGTACCGTGAATGGTTACCATTAGGAGTTGT
GTC
Found at i:22493 original size:22 final size:22
Alignment explanation
Indices: 22468--22510 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
22458 TTTGATAGTA
22468 AGATATTTGTATATGATTAGGT
1 AGATATTTGTATATGATTAGGT
22490 AGATATTTGTATATGATTAGG
1 AGATATTTGTATATGATTAGG
22511 CAAAAATGGT
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:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (22 bp):
AGATATTTGTATATGATTAGGT
Found at i:24740 original size:27 final size:27
Alignment explanation
Indices: 24697--24748 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
24687 ATAATTAAAT
* *
24697 TCAATTTAAAAATAATATA-ATAAACA
1 TCAAATTAAAAAAAATATATATAAACA
24723 TCAAATTAATAAAAAATATATATAAA
1 TCAAATTAA-AAAAAATATATATAAA
24749 GATTAAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 9 0.41
28 5 0.23
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (27 bp):
TCAAATTAAAAAAAATATATATAAACA
Found at i:34955 original size:20 final size:22
Alignment explanation
Indices: 34921--34961 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
34911 AGTAAATGAC
34921 TTTAAAATTATTAAAATTATTT
1 TTTAAAATTATTAAAATTATTT
34943 TTTAAAA-TA-TAAAATTATT
1 TTTAAAATTATTAAAATTATT
34962 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAATTATTAAAATTATTT
Found at i:34965 original size:29 final size:31
Alignment explanation
Indices: 34923--34995 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
34913 TAAATGACTT
34923 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
*
34952 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
34983 TAAAATTATTAAA
1 TAAAATTATTAAA
34996 TAATTTTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 17 0.41
30 10 0.24
31 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:35002 original size:30 final size:29
Alignment explanation
Indices: 34923--35002 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
34913 TAAATGACTT
*
34923 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
* *
34952 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
34983 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
35003 GATTTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 10 0.23
30 22 0.50
31 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:36236 original size:18 final size:18
Alignment explanation
Indices: 36199--36237 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
36189 AGGTTAATTG
* * *
36199 TGTTTTAATTTTTTTTAT
1 TGTTTTAATTATGTTAAT
36217 TGTTTTAATTATGTTAAT
1 TGTTTTAATTATGTTAAT
36235 TGT
1 TGT
36238 AGGTCCCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (18 bp):
TGTTTTAATTATGTTAAT
Found at i:40292 original size:61 final size:60
Alignment explanation
Indices: 40227--40344 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 60
40217 ACAAAATTGA
* * * * *
40227 ATAATTAAATGATCATTTTGTAACTTTTCATAGTTGGATTACCAAAAAAAGAAATTTACTG
1 ATAATTAAATAACCACTTTGTAACTTTTCATAATTGGA-TAACAAAAAAAGAAATTTACTG
* * * *
40288 ATAATTGAGTAACCACTTTGTAACTTTTCATAATTGGATAACTAAACAAGAAATTTA
1 ATAATTAAATAACCACTTTGTAACTTTTCATAATTGGATAACAAAAAAAGAAATTTA
40345 AGTTTACCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (60 bp):
ATAATTAAATAACCACTTTGTAACTTTTCATAATTGGATAACAAAAAAAGAAATTTACTG
Found at i:40647 original size:28 final size:28
Alignment explanation
Indices: 40584--40640 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
40574 ATCTAATATA
40584 TTGCATTCATTAAATTGGCAGGTAATGG
1 TTGCATTCATTAAATTGGCAGGTAATGG
40612 TTGCATTCATTAAATTGGCAGGTAATGG
1 TTGCATTCATTAAATTGGCAGGTAATGG
40640 T
1 T
40641 GCCATTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.37
Consensus pattern (28 bp):
TTGCATTCATTAAATTGGCAGGTAATGG
Found at i:42610 original size:24 final size:24
Alignment explanation
Indices: 42559--42613 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
42549 TTTTTTAGTT
* * *
42559 AAACGCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTATTTCAATC
* *
42583 AAACTCTGTTTATTTATTTGAGTC
1 AAACTCTGTTTATTTATTTCAATC
42607 AAACTCT
1 AAACTCT
42614 TGTTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:57418 original size:14 final size:14
Alignment explanation
Indices: 57399--57441 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
57389 GGGTGTCCAA
57399 TTTTTCTGGAGTTG
1 TTTTTCTGGAGTTG
*
57413 TTTTTCT-GTGTT-
1 TTTTTCTGGAGTTG
*
57425 TTATTCTGGAGTTG
1 TTTTTCTGGAGTTG
57439 TTT
1 TTT
57442 ATTTGTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 6 0.26
13 8 0.35
14 9 0.39
ACGTcount: A:0.07, C:0.07, G:0.23, T:0.63
Consensus pattern (14 bp):
TTTTTCTGGAGTTG
Found at i:57823 original size:24 final size:25
Alignment explanation
Indices: 57777--57823 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
57767 AAAATATCAA
*
57777 ATCAAAATAGTAATCACCCATTTAT
1 ATCAAAATAGTAATCACCAATTTAT
* *
57802 ATCAGAATAG-AATCTCCAATTT
1 ATCAAAATAGTAATCACCAATTT
57824 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (25 bp):
ATCAAAATAGTAATCACCAATTTAT
Found at i:65868 original size:16 final size:16
Alignment explanation
Indices: 65847--65878 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
65837 GATTTATACT
65847 TTCAAGAGCCTAACCC
1 TTCAAGAGCCTAACCC
65863 TTCAAGAGCCTAACCC
1 TTCAAGAGCCTAACCC
65879 AAAGTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.12, T:0.19
Consensus pattern (16 bp):
TTCAAGAGCCTAACCC
Done.